From f7f5c826de552469796096f6317d786a2ae428ed Mon Sep 17 00:00:00 2001
From: Albert <ratschinski.albert@gmail.com>
Date: Mon, 15 Jan 2024 15:21:38 +0100
Subject: [PATCH 1/9] Added Seqprep to the tools

---
 tools/seqprep/.shed.yml                       |  13 +
 tools/seqprep/README.md                       |  15 +
 tools/seqprep/macros.xml                      |  19 +
 tools/seqprep/seqprep.xml                     | 326 ++++++++++++++++++
 tools/seqprep/seqprepFinal.xml                | 301 ++++++++++++++++
 tools/seqprep/test-data/empty1.fq             |   0
 tools/seqprep/test-data/empty2.fq             |   0
 .../test-data/empty_merged_output.fq.gz       | Bin 0 -> 20 bytes
 tools/seqprep/test-data/empty_output1.fq.gz   | Bin 0 -> 20 bytes
 tools/seqprep/test-data/empty_output2.fq.gz   | Bin 0 -> 20 bytes
 tools/seqprep/test-data/input1.fq             | 240 +++++++++++++
 tools/seqprep/test-data/input2.fq             | 240 +++++++++++++
 tools/seqprep/test-data/merged_output.fq.gz   | Bin 0 -> 3132 bytes
 tools/seqprep/test-data/output1.fq.gz         | Bin 0 -> 2286 bytes
 .../test-data/output1_adapter_trim.fq.gz      | Bin 0 -> 5757 bytes
 .../test-data/output1_general_args.fq.gz      | Bin 0 -> 4919 bytes
 tools/seqprep/test-data/output2.fq.gz         | Bin 0 -> 2296 bytes
 .../test-data/output2_adapter_trim.fq.gz      | Bin 0 -> 5899 bytes
 .../test-data/output2_general_args.fq.gz      | Bin 0 -> 5034 bytes
 tools/seqprep/test-data/outputNoMerge1.fq.gz  | Bin 0 -> 4919 bytes
 tools/seqprep/test-data/outputNoMerge2.fq.gz  | Bin 0 -> 5034 bytes
 21 files changed, 1154 insertions(+)
 create mode 100644 tools/seqprep/.shed.yml
 create mode 100644 tools/seqprep/README.md
 create mode 100644 tools/seqprep/macros.xml
 create mode 100644 tools/seqprep/seqprep.xml
 create mode 100644 tools/seqprep/seqprepFinal.xml
 create mode 100644 tools/seqprep/test-data/empty1.fq
 create mode 100644 tools/seqprep/test-data/empty2.fq
 create mode 100644 tools/seqprep/test-data/empty_merged_output.fq.gz
 create mode 100644 tools/seqprep/test-data/empty_output1.fq.gz
 create mode 100644 tools/seqprep/test-data/empty_output2.fq.gz
 create mode 100644 tools/seqprep/test-data/input1.fq
 create mode 100644 tools/seqprep/test-data/input2.fq
 create mode 100644 tools/seqprep/test-data/merged_output.fq.gz
 create mode 100644 tools/seqprep/test-data/output1.fq.gz
 create mode 100644 tools/seqprep/test-data/output1_adapter_trim.fq.gz
 create mode 100644 tools/seqprep/test-data/output1_general_args.fq.gz
 create mode 100644 tools/seqprep/test-data/output2.fq.gz
 create mode 100644 tools/seqprep/test-data/output2_adapter_trim.fq.gz
 create mode 100644 tools/seqprep/test-data/output2_general_args.fq.gz
 create mode 100644 tools/seqprep/test-data/outputNoMerge1.fq.gz
 create mode 100644 tools/seqprep/test-data/outputNoMerge2.fq.gz

diff --git a/tools/seqprep/.shed.yml b/tools/seqprep/.shed.yml
new file mode 100644
index 00000000000..07cc64e01fa
--- /dev/null
+++ b/tools/seqprep/.shed.yml
@@ -0,0 +1,13 @@
+name: seqprep
+owner: iuc
+description: Tool for merging paired-end Illumina reads and trimming adapters.
+homepage_url: https://github.com/jstjohn/SeqPrep
+long_description: |
+    SeqPrep is a program designed to merge paired-end Illumina reads that are overlapping into a single longer read and to trim adapters.
+    It is particularly useful for preparing reads for downstream applications like genome assembly and SNP calling.
+    The tool works by identifying and merging reads that are overlapping and trimming adapters based on user-defined sequences or default parameters.
+  remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep
+categories:
+- Sequence Analysis
+- RNA
+- Preprocessing
diff --git a/tools/seqprep/README.md b/tools/seqprep/README.md
new file mode 100644
index 00000000000..5f3f7c7f2c6
--- /dev/null
+++ b/tools/seqprep/README.md
@@ -0,0 +1,15 @@
+# SeqPrep Tool Documentation
+
+## Overview
+
+SeqPrep is a bioinformatics tool primarily used for processing paired-end Illumina reads. It excels in merging overlapping reads and trimming adapter sequences, making it a valuable asset in genomic sequence analysis. Its efficient handling of paired-end data ensures high-quality preparation for downstream analysis.
+
+## Key Features
+
+- **Read Merging**: Seamlessly merges overlapping paired-end Illumina reads into longer, single reads.
+- **Adapter Trimming**: Efficiently trims adapter sequences from read ends to improve data quality.
+- **Quality Control**: Offers options for quality score cutoff and minimum read length, enhancing the integrity of output data.
+
+## Usage
+
+For a detailed tutorial on how to use SeqPrep, please refer to the [SeqPrep Tutorial](https://github.com/jstjohn/SeqPrep/tree/master).
diff --git a/tools/seqprep/macros.xml b/tools/seqprep/macros.xml
new file mode 100644
index 00000000000..141ca993f68
--- /dev/null
+++ b/tools/seqprep/macros.xml
@@ -0,0 +1,19 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.3.2</token>
+    <token name="@VERSION_SUFFIX@">8</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">seqprep</requirement>
+        </requirements>
+    </xml>
+    <xml name="biotools">
+        <xrefs>
+            <xref type="bio.tools">seqprep</xref>
+        </xrefs>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1134/S1021443716020175</citation>
+        </citations>
+    </xml>
+</macros>
diff --git a/tools/seqprep/seqprep.xml b/tools/seqprep/seqprep.xml
new file mode 100644
index 00000000000..d8e4edad15e
--- /dev/null
+++ b/tools/seqprep/seqprep.xml
@@ -0,0 +1,326 @@
+<tool id="seqprep" name="Merging paired-end Illumina reads (SeqPrep)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description>Merge and Trim Adapter Sequences from Paired-End Illumina Reads</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        SeqPrep
+            -f '${input1}'
+            -r '${input2}'
+            -1 '${output1}'
+            -2 '${output2}'
+
+            #if $merge_reads
+                -s '${merged}'
+            #end if
+
+            ## General Arguments ##
+            #if $general_options.first_read_discarded
+                -3 $general_options.first_read_discarded
+            #end if
+            #if $general_options.second_read_discarded
+                -4 $general_options.second_read_discarded
+            #end if
+            #if $general_options.phred64
+                -6 $general_options.phred64
+            #end if
+            #if $general_options.quality_cutoff
+                -q $general_options.quality_cutoff
+            #end if
+            #if $general_options.min_length
+                -L $general_options.min_length
+            #end if
+
+            ## Additional Adapter/Primer Trimming Arguments ##
+            #if $trimming_options.adapter_a
+                -A $trimming_options.adapter_a
+            #end if
+            #if $trimming_options.adapter_b
+                -B $trimming_options.adapter_b
+            #end if
+            #if $trimming_options.adapter_overlap
+                -O $trimming_options.adapter_overlap
+            #end if
+            #if $trimming_options.max_mismatch_fraction
+                -M $trimming_options.max_mismatch_fraction
+            #end if
+            #if $trimming_options.min_match_fraction
+                -N $trimming_options.min_match_fraction
+            #end if
+            #if $trimming_options.adapter_bandwidth
+                -b $trimming_options.adapter_bandwidth
+            #end if
+            #if $trimming_options.gap_open
+                -Q $trimming_options.gap_open
+            #end if
+            #if $trimming_options.gap_extend
+                -t $trimming_options.gap_extend
+            #end if
+            #if $trimming_options.gap_end
+                -e $trimming_options.gap_end
+            #end if
+            #if $trimming_options.local_alignment_score
+                -Z $trimming_options.local_alignment_score
+            #end if
+            #if $trimming_options.read_alignment_bandwidth
+                -w $trimming_options.read_alignment_bandwidth
+            #end if
+            #if $trimming_options.read_alignment_gap_open
+                -W $trimming_options.read_alignment_gap_open
+            #end if
+            #if $trimming_options.read_alignment_gap_extend
+                -p $trimming_options.read_alignment_gap_extend
+            #end if
+            #if $trimming_options.read_alignment_gap_end
+                -P $trimming_options.read_alignment_gap_end
+            #end if
+            #if $trimming_options.read_alignment_max_gap_fraction
+                -X $trimming_options.read_alignment_max_gap_fraction
+            #end if
+
+            ## Additional Arguments for Merging ##
+            #if $merging_options.maximum_quality_score
+                -y $merging_options.maximum_quality_score
+            #end if
+            #if $merging_options.print_overhang
+                -g $merging_options.print_overhang
+            #end if
+            #if $merging_options.min_base_pair_overlap
+                -o $merging_options.min_base_pair_overlap
+            #end if
+            #if $merging_options.max_mismatch_fraction
+                -m $merging_options.max_mismatch_fraction
+            #end if
+            #if $merging_options.min_match_fraction
+                -n $merging_options.min_match_fraction
+            #end if
+    ]]></command>
+    <inputs>
+        <param label="First Read Input (FASTQ)" name="input1" type="data" format="fastq" />
+        <param label="Second Read Input (FASTQ)" name="input2" type="data" format="fastq" />
+        <param label="Merge Reads" name="merge_reads" type="boolean" truevalue="true" falsevalue="false" checked="true"/>
+
+        <!-- Section for General Arguments -->
+        <section name="general_options" title="General Arguments (Optional)" expanded="false">
+            <param label="First Read Discarded FASTQ Filename" name="first_read_discarded" argument="-3" type="text" optional="true" help="first read discarded fastq filename" />
+            <param label="Second Read Discarded FASTQ Filename" name="second_read_discarded" argument="-4" type="text" optional="true" help="second read discarded fastq filename" />
+            <param label="Input Sequence is in Phred+64 Format" name="phred64" argument="-6" type="boolean" truevalue="-6" falsevalue="" checked="false" help="Input sequence is in phred+64 rather than phred+33 format, the output will still be phred+33"/>
+            <param label="Quality Score Cutoff" name="quality_cutoff" argument="-q" type="integer" optional="true" value="13" help="Quality score cutoff for mismatches to be counted in overlap" />
+            <param label="Minimum Length of Reads" name="min_length" argument="-L" type="integer" optional="true" value="30" help="Minimum length of a trimmed or merged read to print it" />
+        </section>
+
+        <!-- Section for Additional Adapter/Primer Trimming Arguments -->
+        <section name="trimming_options" title="Additional Adapter/Primer Trimming Arguments" expanded="false">
+            <param name="adapter_a" argument="-A" label="Adapter Sequence A" type="text" optional="true" value="AGATCGGAAGAGCGGTTCAG" help="Forward read primer/adapter sequence to trim as it would appear at the end of a read" />
+            <param name="adapter_b" argument="-B" label="Adapter Sequence B" type="text" optional="true" value="AGATCGGAAGAGCGTCGTGT" help="Reverse read primer/adapter sequence to trim as it would appear at the end of a read" />
+            <param name="adapter_overlap" argument="-O" label="Minimum Overall Base Pair Overlap with Adapter" type="integer" value="10" optional="true" help="minimum overall base pair overlap with adapter sequence to trim" />
+            <param name="max_mismatch_fraction" argument="-M" label="Maximum Fraction of Good Quality Mismatching Bases" type="float" value="0.02" optional="true" help="maximum fraction of good quality mismatching bases for primer/adapter overlap" />
+            <param name="min_match_fraction" argument="-N" label="Minimum Fraction of Matching Bases" type="float" value="0.87" optional="true" help="minimum fraction of matching bases for primer/adapter overlap" />
+            <param name="adapter_bandwidth" argument="-b" label="Adapter Alignment Band-width" type="integer" value="50" optional="true" />
+            <param name="gap_open" argument="-Q" label="Adapter Alignment Gap-Open" type="integer" value="8" optional="true" />
+            <param name="gap_extend" argument="-t" label="Adapter Alignment Gap-Extension" type="integer" value="2" optional="true" />
+            <param name="gap_end" argument="-e" label="Adapter Alignment Gap-End" type="integer" value="2" optional="true" />
+            <param name="local_alignment_score" argument="-Z" label="Minimum Local Alignment Score Cutoff" type="integer" value="26" optional="true" help="Adapter alignment minimum local alignment score cutoff [roughly (2*num_hits) - (num_gaps*gap_open) - (num_gaps*gap_close) - (gap_len*gap_extend) - (2*num_mismatches)]" />
+            <param name="read_alignment_bandwidth" argument="-w" label="Read Alignment Band-width" type="integer" value="50" optional="true" />
+            <param name="read_alignment_gap_open" argument="-W" label="Read Alignment Gap-Open" type="integer" value="26" optional="true" />
+            <param name="read_alignment_gap_extend" argument="-p" label="Read Alignment Gap-Extension" type="integer" value="9" optional="true" />
+            <param name="read_alignment_gap_end" argument="-P" label="Read Alignment Gap-End" type="integer" value="5" optional="true" help="read alignment maximum fraction gap cutoff" />
+            <param name="read_alignment_max_gap_fraction" argument="-X" label="Read Alignment Maximum Fraction Gap Cutoff" type="float" value="0.125" optional="true" />
+        </section>
+
+        <!-- Section for Optional Arguments for Merging: -->
+        <section name="merging_options" title="Optional Arguments for Merging" expanded="false">
+            <param name="maximum_quality_score" argument="-y" label="Maximum Quality Score in Output" type="text" optional="true" help="Maximum quality score in output (phred 33), default = ']'"/>
+            <param name="print_overhang" argument="-g" type="boolean" truevalue="-g" falsevalue="" checked="false" label="Print Overhang When Adapters Are Present and Stripped" help="Use this if reads are different lengths"/>
+            <param name="min_base_pair_overlap" argument="-o" type="integer" optional="true" value="15" label="Minimum Overall Base Pair Overlap" help="Minimum overall base pair overlap to merge two reads"/>
+            <param name="max_mismatch_fraction" argument="-m" type="float" optional="true" value="0.02" label="Maximum Fraction of Good Quality Mismatching Bases" help="Maximum fraction of good quality mismatching bases to overlap reads"/>
+            <param name="min_match_fraction" argument="-n" type="float" optional="true" value="0.9" label="Minimum Fraction of Matching Bases" help="Minimum fraction of matching bases to overlap reads"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data format="fastq.gz" name="output1" label="${tool.name} on ${on_string}: First Read Output">
+            <filter>output_all</filter>
+        </data>
+        <data format="fastq.gz" name="output2" label="${tool.name} on ${on_string}: Second Read Output">
+            <filter>output_all</filter>
+        </data>
+        <data format="fastq.gz" name="merged" label="${tool.name} on ${on_string}: Merged Reads">
+            <filter>merge_reads</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!-- Test default inputs #1 -->
+        <test expect_num_outputs="3">
+            <param name="input1" value="input1.fq" />
+            <param name="input2" value="input2.fq" />
+            <param name="merge_reads" value="true" />
+
+            <!-- Section for General Arguments -->
+            <section name="general_options" >
+                <param name="quality_cutoff" value="13" />
+                <param name="min_length" value="30" />
+            </section>
+
+            <!-- Section for Additional Adapter/Primer Trimming Arguments -->
+            <section name="trimming_options">
+                <param name="adapter_a" value="AGATCGGAAGAGCGGTTCAG" />
+                <param name="adapter_b" value="AGATCGGAAGAGCGTCGTGT" />
+                <param name="adapter_overlap" value="10" /> 
+                <param name="max_mismatch_fraction" value="0.02" />
+                <param name="min_match_fraction" value="0.87" />
+                <param name="adapter_bandwidth" value="50" />
+                <param name="gap_open" value="8" />
+                <param name="gap_extend" value="2" />
+                <param name="gap_end" value="2" />
+                <param name="local_alignment_score" value="26" />
+                <param name="read_alignment_bandwidth" value="50" />
+                <param name="read_alignment_gap_open" value="26" />
+                <param name="read_alignment_gap_extend" value="9" />
+                <param name="read_alignment_gap_end" value="5" />
+                <param name="read_alignment_max_gap_fraction" value="0.125" />
+            </section>
+
+            <!-- Outputs -->
+            <output name="output1" file="output1.fq.gz" />
+            <output name="output2" file="output2.fq.gz" />
+            <output name="merged" file="merged_output.fq.gz" />
+        </test>
+    
+        <!-- Without Merging, Two Outputs #2 -->
+        <test expect_num_outputs="2">
+            <param name="input1" value="input1.fq" />
+            <param name="input2" value="input2.fq" />
+            <param name="merge_reads" value="false" />
+
+            <!-- Section for General Arguments -->
+            <section name="general_options" >
+                <param name="quality_cutoff" value="13" />
+                <param name="min_length" value="30" />
+            </section>  
+
+            <!-- Section for Additional Adapter/Primer Trimming Arguments -->
+            <section name="trimming_options">
+                <param name="adapter_a" value="AGATCGGAAGAGCGGTTCAG" />
+                <param name="adapter_b" value="AGATCGGAAGAGCGTCGTGT" />
+                <param name="adapter_overlap" value="10" /> 
+                <param name="max_mismatch_fraction" value="0.02" />
+                <param name="min_match_fraction" value="0.87" />
+                <param name="adapter_bandwidth" value="50" />
+                <param name="gap_open" value="8" />
+                <param name="gap_extend" value="2" />
+                <param name="gap_end" value="2" />
+                <param name="local_alignment_score" value="26" />
+                <param name="read_alignment_bandwidth" value="50" />
+                <param name="read_alignment_gap_open" value="26" />
+                <param name="read_alignment_gap_extend" value="9" />
+                <param name="read_alignment_gap_end" value="5" />
+                <param name="read_alignment_max_gap_fraction" value="0.125" />
+            </section>
+
+            <!-- Outputs -->
+            <output name="output1" file="outputNoMerge1.fq.gz" />
+            <output name="output2" file="outputNoMerge2.fq.gz" />
+        </test>
+
+        <!-- Test with Empty Input Files #3 -->
+        <test expect_num_outputs="3">
+            <param name="input1" value="empty1.fq" />
+            <param name="input2" value="empty2.fq" />
+            <param name="merge_reads" value="true" />
+
+
+            <!-- Section for General Arguments -->
+            <section name="general_options" >
+                <param name="quality_cutoff" value="13" />
+                <param name="min_length" value="30" />
+            </section>  
+
+            <!-- Section for Additional Adapter/Primer Trimming Arguments -->
+            <section name="trimming_options">
+                <param name="adapter_a" value="AGATCGGAAGAGCGGTTCAG" />
+                <param name="adapter_b" value="AGATCGGAAGAGCGTCGTGT" />
+                <param name="adapter_overlap" value="10" /> 
+                <param name="max_mismatch_fraction" value="0.02" />
+                <param name="min_match_fraction" value="0.87" />
+                <param name="adapter_bandwidth" value="50" />
+                <param name="gap_open" value="8" />
+                <param name="gap_extend" value="2" />
+                <param name="gap_end" value="2" />
+                <param name="local_alignment_score" value="26" />
+                <param name="read_alignment_bandwidth" value="50" />
+                <param name="read_alignment_gap_open" value="26" />
+                <param name="read_alignment_gap_extend" value="9" />
+                <param name="read_alignment_gap_end" value="5" />
+                <param name="read_alignment_max_gap_fraction" value="0.125" />
+            </section>
+
+            <!-- Outputs -->
+            <output name="output1" file="empty_output1.fq.gz" />
+            <output name="output2" file="empty_output2.fq.gz" />
+            <output name="merged" file="empty_merged_output.fq.gz" />
+        </test>
+
+        <!-- Advanced Functional Tests -->
+        <!-- General Arguments Test #4 -->
+        <test expect_num_outputs="2">
+            <param name="input1" value="input1.fq" />
+            <param name="input2" value="input2.fq" />
+            <param name="merge_reads" value="false" />
+
+            <param name="quality_cutoff" value="15" />
+            <param name="min_length" value="25" />
+
+            <!-- Outputs -->
+            <output name="output1" file="output1_general_args.fq.gz" />
+            <output name="output2" file="output2_general_args.fq.gz" />
+        </test>
+
+        <!-- Adapter/Primer Trimming Arguements Test #5 -->
+        <test expect_num_outputs="2">
+            <param name="input1" value="input1.fq" />
+            <param name="input2" value="input2.fq" />
+            <section name="trimming_options">
+                <param name="adapter_a" value="ACTGACTG" />
+                <param name="adapter_b" value="GTGACTGA" />
+                <param name="adapter_overlap" value="12" />
+                <param name="max_mismatch_fraction" value="0.03" />
+                <param name="min_match_fraction" value="0.85" />
+                <param name="adapter_bandwidth" value="55" />
+                <param name="gap_open" value="10" />
+                <param name="gap_extend" value="3" />
+                <param name="gap_end" value="3" />
+                <param name="local_alignment_score" value="28" />
+            </section>
+
+            <!-- Outputs -->
+            <output name="output1" file="output1_adapter_trim.fq.gz" />
+            <output name="output2" file="output2_adapter_trim.fq.gz" />
+        </test>
+    </tests>
+    <help><![CDATA[
+    **SeqPrep**
+    
+    SeqPrep is a versatile tool designed for merging overlapping paired-end Illumina reads into a single, longer read. Additionally, it offers the functionality to trim adapter sequences from reads, making it an needful tool for preprocessing Illumina sequencing data.
+
+    **Usage**
+
+    To utilize SeqPrep, start by selecting your input FASTQ files: one for the first set of reads and another for the second set. SeqPrep provides several options to customize your data processing:
+
+    - **Adapter Sequences:** You can provide specific sequences for adapter trimming if they are known. SeqPrep will remove these sequences from the reads.
+    - **Quality Score Cutoff:** Set a threshold for the quality score. Reads with quality scores below this threshold can be discarded or trimmed.
+    - **Minimum Read Length:** Define the minimum length for reads to be retained after trimming. Reads shorter than this length will be discarded.
+
+    If the merging feature is enabled, SeqPrep will combine overlapping reads into longer sequences, thereby enhancing the data quality for downstream analysis.
+
+    **Outputs**
+
+    SeqPrep generates outputs in gzipped FASTQ format. Depending on your settings, this may include:
+
+    - Individual read files (if they are not fully merged).
+    - A combined read file with merged reads.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file
diff --git a/tools/seqprep/seqprepFinal.xml b/tools/seqprep/seqprepFinal.xml
new file mode 100644
index 00000000000..7fa6a844f84
--- /dev/null
+++ b/tools/seqprep/seqprepFinal.xml
@@ -0,0 +1,301 @@
+<tool id="seqprep" name="Merging paired-end Illumina reads (SeqPrep)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description>Merge and Trim Adapter Sequences from Paired-End Illumina Reads</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        SeqPrep
+            -f '${input1}'
+            -r '${input2}'
+            -1 '${output1}'
+            -2 '${output2}'
+
+            #if $merge_reads
+                -s '${merged}'
+            #end if
+
+            ## General Arguments ##
+            #if $general_options.first_read_discarded
+                -3 $general_options.first_read_discarded
+            #end if
+            #if $general_options.second_read_discarded
+                -4 $general_options.second_read_discarded
+            #end if
+            #if $general_options.phred64
+                -6 $general_options.phred64
+            #end if
+            #if $general_options.quality_cutoff
+                -q $general_options.quality_cutoff
+            #end if
+            #if $general_options.min_length
+                -L $general_options.min_length
+            #end if
+
+            ## Additional Adapter/Primer Trimming Arguments ##
+
+            #if $trimming_options.adapter_a
+                -A $trimming_options.adapter_a
+            #end if
+            #if $trimming_options.adapter_b
+                -B $trimming_options.adapter_b
+            #end if
+            #if $trimming_options.adapter_overlap
+                -O $trimming_options.adapter_overlap
+            #end if
+            #if $trimming_options.max_mismatch_fraction
+                -M $trimming_options.max_mismatch_fraction
+            #end if
+            #if $trimming_options.min_match_fraction
+                -N $trimming_options.min_match_fraction
+            #end if
+            #if $trimming_options.adapter_bandwidth
+                -b $trimming_options.adapter_bandwidth
+            #end if
+            #if $trimming_options.gap_open
+                -Q $trimming_options.gap_open
+            #end if
+            #if $trimming_options.gap_extend
+                -t $trimming_options.gap_extend
+            #end if
+            #if $trimming_options.gap_end
+                -e $trimming_options.gap_end
+            #end if
+            #if $trimming_options.local_alignment_score
+                -Z $trimming_options.local_alignment_score
+            #end if
+            #if $trimming_options.read_alignment_bandwidth
+                -w $trimming_options.read_alignment_bandwidth
+            #end if
+            #if $trimming_options.read_alignment_gap_open
+                -W $trimming_options.read_alignment_gap_open
+            #end if
+            #if $trimming_options.read_alignment_gap_extend
+                -p $trimming_options.read_alignment_gap_extend
+            #end if
+            #if $trimming_options.read_alignment_gap_end
+                -P $trimming_options.read_alignment_gap_end
+            #end if
+            #if $trimming_options.read_alignment_max_gap_fraction
+                -X $trimming_options.read_alignment_max_gap_fraction
+            #end if
+    ]]></command>
+    <inputs>
+        <param label="First Read Input (FASTQ)" name="input1" type="data" format="fastq" />
+        <param label="Second Read Input (FASTQ)" name="input2" type="data" format="fastq" />
+        <param label="Merge Reads" name="merge_reads" type="boolean" truevalue="true" falsevalue="false" />
+
+        <!-- Section for General Arguments -->
+        <section name="general_options" title="General Arguments (Optional)" expanded="false">
+            <param label="First Read Discarded FASTQ Filename" name="first_read_discarded" argument="-3" type="text" optional="true" help="first read discarded fastq filename" />
+            <param label="Second Read Discarded FASTQ Filename" name="second_read_discarded" argument="-4" type="text" optional="true" help="second read discarded fastq filename" />
+            <param label="Input Sequence is in Phred+64 Format" name="phred64" argument="-6" type="boolean" truevalue="-6" falsevalue="" checked="false" help="Input sequence is in phred+64 rather than phred+33 format, the output will still be phred+33"/>
+            <param label="Quality Score Cutoff" name="quality_cutoff" argument="-q" type="integer" optional="true" value="13" help="Quality score cutoff for mismatches to be counted in overlap" />
+            <param label="Minimum Length of Reads" name="min_length" argument="-L" type="integer" optional="true" value="30" help="Minimum length of a trimmed or merged read to print it" />
+        </section>
+
+        <!-- Section for Additional Adapter/Primer Trimming Arguments -->
+        <section name="trimming_options" title="Additional Adapter/Primer Trimming Arguments" expanded="false">
+            <param name="adapter_a" argument="-A" label="Adapter Sequence A" type="text" optional="true" value="AGATCGGAAGAGCGGTTCAG" help="Forward read primer/adapter sequence to trim as it would appear at the end of a read" />
+            <param name="adapter_b" argument="-B" label="Adapter Sequence B" type="text" optional="true" value="AGATCGGAAGAGCGTCGTGT" help="Reverse read primer/adapter sequence to trim as it would appear at the end of a read" />
+            <param name="adapter_overlap" argument="-O" label="Minimum Overall Base Pair Overlap with Adapter" type="integer" value="10" optional="true" help="minimum overall base pair overlap with adapter sequence to trim" />
+            <param name="max_mismatch_fraction" argument="-M" label="Maximum Fraction of Good Quality Mismatching Bases" type="float" value="0.02" optional="true" help="maximum fraction of good quality mismatching bases for primer/adapter overlap" />
+            <param name="min_match_fraction" argument="-N" label="Minimum Fraction of Matching Bases" type="float" value="0.87" optional="true" help="minimum fraction of matching bases for primer/adapter overlap" />
+            <param name="adapter_bandwidth" argument="-b" label="Adapter Alignment Band-width" type="integer" value="50" optional="true" />
+            <param name="gap_open" argument="-Q" label="Adapter Alignment Gap-Open" type="integer" value="8" optional="true" />
+            <param name="gap_extend" argument="-t" label="Adapter Alignment Gap-Extension" type="integer" value="2" optional="true" />
+            <param name="gap_end" argument="-e" label="Adapter Alignment Gap-End" type="integer" value="2" optional="true" />
+            <param name="local_alignment_score" argument="-Z" label="Minimum Local Alignment Score Cutoff" type="integer" value="26" optional="true" help="Adapter alignment minimum local alignment score cutoff [roughly (2*num_hits) - (num_gaps*gap_open) - (num_gaps*gap_close) - (gap_len*gap_extend) - (2*num_mismatches)]" />
+            <param name="read_alignment_bandwidth" argument="-w" label="Read Alignment Band-width" type="integer" value="50" optional="true" />
+            <param name="read_alignment_gap_open" argument="-W" label="Read Alignment Gap-Open" type="integer" value="26" optional="true" />
+            <param name="read_alignment_gap_extend" argument="-p" label="Read Alignment Gap-Extension" type="integer" value="9" optional="true" />
+            <param name="read_alignment_gap_end" argument="-P" label="Read Alignment Gap-End" type="integer" value="5" optional="true" help="read alignment maximum fraction gap cutoff" />
+            <param name="read_alignment_max_gap_fraction" argument="-X" label="Read Alignment Maximum Fraction Gap Cutoff" type="float" value="0.125" optional="true" />
+        </section>
+    </inputs>
+    <outputs>
+        <data format="fastq.gz" name="output1" label="${tool.name} on ${on_string}: First Read Output">
+            <filter>output_all</filter>
+        </data>
+        <data format="fastq.gz" name="output2" label="${tool.name} on ${on_string}: Second Read Output">
+            <filter>output_all</filter>
+        </data>
+        <data format="fastq.gz" name="merged" label="${tool.name} on ${on_string}: Merged Reads">
+            <filter>merge_reads</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!-- Test default inputs #1 -->
+        <test expect_num_outputs="3">
+            <param name="input1" value="input1.fq" />
+            <param name="input2" value="input2.fq" />
+            <param name="merge_reads" value="true" />
+
+            <!-- Section for General Arguments -->
+            <section name="general_options" >
+                <param name="quality_cutoff" value="13" />
+                <param name="min_length" value="30" />
+            </section>
+
+            <!-- Section for Additional Adapter/Primer Trimming Arguments -->
+            <section name="trimming_options">
+                <param name="adapter_a" value="AGATCGGAAGAGCGGTTCAG" />
+                <param name="adapter_b" value="AGATCGGAAGAGCGTCGTGT" />
+                <param name="adapter_overlap" value="10" /> 
+                <param name="max_mismatch_fraction" value="0.02" />
+                <param name="min_match_fraction" value="0.87" />
+                <param name="adapter_bandwidth" value="50" />
+                <param name="gap_open" value="8" />
+                <param name="gap_extend" value="2" />
+                <param name="gap_end" value="2" />
+                <param name="local_alignment_score" value="26" />
+                <param name="read_alignment_bandwidth" value="50" />
+                <param name="read_alignment_gap_open" value="26" />
+                <param name="read_alignment_gap_extend" value="9" />
+                <param name="read_alignment_gap_end" value="5" />
+                <param name="read_alignment_max_gap_fraction" value="0.125" />
+            </section>
+
+            <!-- Outputs -->
+            <output name="output1" file="output1.fq.gz" />
+            <output name="output2" file="output2.fq.gz" />
+            <output name="merged" file="merged_output.fq.gz" />
+        </test>
+    
+        <!-- Without Merging, Two Outputs #2 -->
+        <test expect_num_outputs="2">
+            <param name="input1" value="input1.fq" />
+            <param name="input2" value="input2.fq" />
+            <param name="merge_reads" value="false" />
+
+            <!-- Section for General Arguments -->
+            <section name="general_options" >
+                <param name="quality_cutoff" value="13" />
+                <param name="min_length" value="30" />
+            </section>  
+
+            <!-- Section for Additional Adapter/Primer Trimming Arguments -->
+            <section name="trimming_options">
+                <param name="adapter_a" value="AGATCGGAAGAGCGGTTCAG" />
+                <param name="adapter_b" value="AGATCGGAAGAGCGTCGTGT" />
+                <param name="adapter_overlap" value="10" /> 
+                <param name="max_mismatch_fraction" value="0.02" />
+                <param name="min_match_fraction" value="0.87" />
+                <param name="adapter_bandwidth" value="50" />
+                <param name="gap_open" value="8" />
+                <param name="gap_extend" value="2" />
+                <param name="gap_end" value="2" />
+                <param name="local_alignment_score" value="26" />
+                <param name="read_alignment_bandwidth" value="50" />
+                <param name="read_alignment_gap_open" value="26" />
+                <param name="read_alignment_gap_extend" value="9" />
+                <param name="read_alignment_gap_end" value="5" />
+                <param name="read_alignment_max_gap_fraction" value="0.125" />
+            </section>
+
+            <!-- Outputs -->
+            <output name="output1" file="outputNoMerge1.fq.gz" />
+            <output name="output2" file="outputNoMerge2.fq.gz" />
+        </test>
+
+        <!-- Test with Empty Input Files #3 -->
+        <test expect_num_outputs="3">
+            <param name="input1" value="empty1.fq" />
+            <param name="input2" value="empty2.fq" />
+            <param name="merge_reads" value="true" />
+
+
+            <!-- Section for General Arguments -->
+            <section name="general_options" >
+                <param name="quality_cutoff" value="13" />
+                <param name="min_length" value="30" />
+            </section>  
+
+            <!-- Section for Additional Adapter/Primer Trimming Arguments -->
+            <section name="trimming_options">
+                <param name="adapter_a" value="AGATCGGAAGAGCGGTTCAG" />
+                <param name="adapter_b" value="AGATCGGAAGAGCGTCGTGT" />
+                <param name="adapter_overlap" value="10" /> 
+                <param name="max_mismatch_fraction" value="0.02" />
+                <param name="min_match_fraction" value="0.87" />
+                <param name="adapter_bandwidth" value="50" />
+                <param name="gap_open" value="8" />
+                <param name="gap_extend" value="2" />
+                <param name="gap_end" value="2" />
+                <param name="local_alignment_score" value="26" />
+                <param name="read_alignment_bandwidth" value="50" />
+                <param name="read_alignment_gap_open" value="26" />
+                <param name="read_alignment_gap_extend" value="9" />
+                <param name="read_alignment_gap_end" value="5" />
+                <param name="read_alignment_max_gap_fraction" value="0.125" />
+            </section>
+
+            <!-- Outputs -->
+            <output name="output1" file="empty_output1.fq.gz" />
+            <output name="output2" file="empty_output2.fq.gz" />
+            <output name="merged" file="empty_merged_output.fq.gz" />
+        </test>
+
+        <!-- Advanced Functional Tests -->
+        <!-- General Arguments Test #4 -->
+        <test expect_num_outputs="2">
+            <param name="input1" value="input1.fq" />
+            <param name="input2" value="input2.fq" />
+            <param name="merge_reads" value="false" />
+
+            <param name="quality_cutoff" value="15" />
+            <param name="min_length" value="25" />
+
+            <!-- Outputs -->
+            <output name="output1" file="output1_general_args.fq.gz" />
+            <output name="output2" file="output2_general_args.fq.gz" />
+        </test>
+
+        <!-- Adapter/Primer Trimming Arguements Test #5 -->
+        <test expect_num_outputs="2">
+            <param name="input1" value="input1.fq" />
+            <param name="input2" value="input2.fq" />
+            <section name="trimming_options">
+                <param name="adapter_a" value="ACTGACTG" />
+                <param name="adapter_b" value="GTGACTGA" />
+                <param name="adapter_overlap" value="12" />
+                <param name="max_mismatch_fraction" value="0.03" />
+                <param name="min_match_fraction" value="0.85" />
+                <param name="adapter_bandwidth" value="55" />
+                <param name="gap_open" value="10" />
+                <param name="gap_extend" value="3" />
+                <param name="gap_end" value="3" />
+                <param name="local_alignment_score" value="28" />
+            </section>
+
+            <!-- Outputs -->
+            <output name="output1" file="output1_adapter_trim.fq.gz" />
+            <output name="output2" file="output2_adapter_trim.fq.gz" />
+        </test>
+    </tests>
+    <help><![CDATA[
+    **SeqPrep**
+    
+    SeqPrep is a versatile tool designed for merging overlapping paired-end Illumina reads into a single, longer read. Additionally, it offers the functionality to trim adapter sequences from reads, making it an needful tool for preprocessing Illumina sequencing data.
+
+    **Usage**
+
+    To utilize SeqPrep, start by selecting your input FASTQ files: one for the first set of reads and another for the second set. SeqPrep provides several options to customize your data processing:
+
+    - **Adapter Sequences:** You can provide specific sequences for adapter trimming if they are known. SeqPrep will remove these sequences from the reads.
+    - **Quality Score Cutoff:** Set a threshold for the quality score. Reads with quality scores below this threshold can be discarded or trimmed.
+    - **Minimum Read Length:** Define the minimum length for reads to be retained after trimming. Reads shorter than this length will be discarded.
+
+    If the merging feature is enabled, SeqPrep will combine overlapping reads into longer sequences, thereby enhancing the data quality for downstream analysis.
+
+    **Outputs**
+
+    SeqPrep generates outputs in gzipped FASTQ format. Depending on your settings, this may include:
+
+    - Individual read files (if they are not fully merged).
+    - A combined read file with merged reads.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file
diff --git a/tools/seqprep/test-data/empty1.fq b/tools/seqprep/test-data/empty1.fq
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/tools/seqprep/test-data/empty2.fq b/tools/seqprep/test-data/empty2.fq
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/tools/seqprep/test-data/empty_merged_output.fq.gz b/tools/seqprep/test-data/empty_merged_output.fq.gz
new file mode 100644
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diff --git a/tools/seqprep/test-data/empty_output2.fq.gz b/tools/seqprep/test-data/empty_output2.fq.gz
new file mode 100644
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diff --git a/tools/seqprep/test-data/input1.fq b/tools/seqprep/test-data/input1.fq
new file mode 100644
index 00000000000..a926e0df40c
--- /dev/null
+++ b/tools/seqprep/test-data/input1.fq
@@ -0,0 +1,240 @@
+@SimSeq_1/229/1
+TAGGAGGCTTGGGGTTAGGAATTGGTCAAATAGGTTTATGTTCAAGGTCAGGGTCATGTTTTAATAGTTATGGCTTTGTAAGGGGTTGGGCTGCTTGTGA
++
+E=AGEFGGGFFEDDGGGECGDADF>DEF?EECAFFEBF:=B2EGGEGF#ABAF7BGFC:FC??:D:?FCD<A??EB5E:G##EEDAB;###.#@EE?BD#
+@SimSeq_2/49/1
+AAAGAAATTAGGTTTAAATTCCAAGCCGAGGGCCTTCAAAGCCCTAAATAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAAA
++
+F?A?BEEDAGAGFFGBFDE>E=G;FD=ED<CFGDGEGFG7DF5DFGBEGBCBEFCBCEDC+CEBE7D##?,=#5BD+D#:?EGC::#5,#E5=9+D#EF#
+@SimSeq_3/149/1
+GAAAATTAATAGCACTATCGTCCATTGCCCAAATAGCATGAATTATCGTAATTATTAAATACGCACCATCACTAGCCATCCTAACCTTCTACATCTGCTC
++
+EDGBGFEEG>:FGD=GG5F?CFEEEFED,?:?D:GFGDEEFDEEDEDFFAEAE@?E>BGEFE3EA@1GED#=#-5:CEAC#?4DBGE?F#FAFD#C#C#G
+@SimSeq_4/197/1
+CGGGGGCCTAACTGGGATTGTCCTAGCCAACTCCTCACTAGACATTGTCCTCCACGACACGTATTATGTAGTGGCCCACTTCCACTACGTACTCTCAATA
++
+GDEGGDEGFGGDEGCFE>F>E;G>F@CFGGGFBGEDGDEC@GGEFG>ACBEFGGEE?F?@(G7GEFCG#E#B@A?CE;FE?G:3#7:B?=,F;D@>A##D
+@SimSeq_5/40/1
+ACCCCTCTCAGAGGAGGATGGAGCATGGTGGTATTGCGGCAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAAAAAAAAAAGA
++
+CFGGD>AFGGGFGEEDGGE?EFDGEGBFEBED+FBG5GGFE:BEAADABEF@?EEEBBF;+DDEDD3=E#F2#)G*#C>>F3>E#@C#?4<G#-BE:?#7
+@SimSeq_6/190/1
+TAACTAAATATTTGTGAGATCGAAGCTCGCCTGTTTATTGAGGTTTTAGCTTAATTAAAGTTTCTGAGTTGCACTTTGAAGATGCCGGATAGAGTCCTGC
++
+DFD:DAE?GE0FDCAFF:GE>DFF;G6G@FGGEEGFD@EGAED=G7E1G:EFGEFD>BGD@:DE?#;(G3=8#:DDBD6#AG##E#@E:8BGG#/DG#<B
+@SimSeq_7/178/1
+TAAATCCCATTCCACCCCTACTTCACCATAAAAGACGCCCTAGGAGCAGCACTAGCTGCCTCCTCACTACTCATCTTAGCTCTCTACCTACCAGCCCTAT
++
+:BFCBD@GGFEFGF>AGDDF5EGGFAGGD@DFFDD@G??GF>BEBDE4EGAEFADFE@G:A#GFD=C#BBG#BGF#CEC=F>8:#E<FG5E>E=5DE#:#
+@SimSeq_8/18/1
+AATCCTCCCTCCCCTTATAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+@A8GG?DDFEFCBGGGADFE<7EEFDG>>EGGEDBGAEDG:G8DFF@FG5GECCCEF*=BC=,DC?C>CE#D:BD0#=3ED@F#E(AF5GAE4GGF@:,=
+@SimSeq_9/103/1
+GTTGTCCGGTTACTTTAATAGTCAGGCAGGGGTTATTGGTTTCGTCTATGAGGTATAGGGTGCGTAGTGATGGTAGGGCAATTGAGATAAGGACAAAGGC
++
+F;GFDE@?;GF?:5E:CGCGD?@D=GFCEEDC7=EAD#F5G:EGACFDE:*C:FA=BA*<AF;EG=D=CEE7B54C@?C9:=FFB@AG:#E#AB-#DC#F
+@SimSeq_a/334/1
+TTCAAGAAGTAGAAGTAATCTGAACCGTCCTACCAGCCATTGTCCTTATCTCAATTGCCCTACCAGCACTACGCACCCTATACCTCAGAGACGAAACCAA
++
+GG?>AGFGEEFFDGFGCFGDFEGC?F:DEBEGGAGEGEE>EEGAFB)F>EBD-FAA>GG?GFG3B#B6G:EG6;>DEG#2G?GC?D##)GB=#D###ED#
+@SimSeq_b/247/1
+TAACAATAAGGGAGATTCAAACGATTAGGAAGGTTGTTAGTCAAGGTTCTGGGTTTAGTTGTGGCATGGTCACTAAGGGGGAGGGGGTAATACTAGTCCC
++
+G?DGG?B;GC?GEA?E7AACD@EEDE:GE:=GF??6EEGDFGFFBDFBG0EF.DB@D@EE5A@#E2#8ADA6DEE=@3EDEC#C:CCB#EF?FD=#??5#
+@SimSeq_c/0/1
+AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+DFBCGCG7B?BG=CEEEFGGEDBGFAEEGGEFADGFD#:ED>/GG:G:BDDFAD:=EG5@EGDBDE>>8D,BDB3F@BGB#BDD#BB:EE:AD:#DD##>
+@SimSeq_d/127/1
+TTAAGGCTTAAGTAGATGGGGCAGGTTCCTATGCTGAGTCAATGTCAAGTGAATGAGAGGGGAACTATGTTGTTGTAAGTTAATAAAATAAGGGGAGGGA
++
+BFGCCG?E?EG2EBEGGGGCDGFED:FGDDGDGEEF+CGADDGG=G=ADG?=BE5=EGA:F3DAD>ADE@8DG#E#:A#29BF?AEFEED>=;E#DCC?:
+@SimSeq_e/84/1
+CCCCTGTTGTATTTCAACTATAAAAACCCATGACCCACCAACTACGAAAATCCCACCCAATCATTAAACTCATCAACCGCTCCCAGATCGGAAGAGCGGT
++
+BEEFFCFGGGEBG?GE9G>GFEGGCGFEFGBE<EFG>GEGEG@FGBFDE?F-;GF#D#E;@BD?=:??G#DDCF?DGEDDAGBCAC6#F?C#F#475#B#
+@SimSeq_f/64/1
+CTCAGGATTCTTTTCCAAAGACGCTATTATTGAAGCACTAAACACCTCTTATATTAACGCCTGTAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACC
++
+ADG9EGGFDC=DGGGF=DFBDGAGG;B5GGDFA=CCFFBGGF<B85DFGAFGAE#1:DCGE?#EB??584F*?BEDAGDFB#D#EG85?EE,E=E6#C:A
+@SimSeq_10/154/1
+CACATTCGTAAGGGGATAATTTTTCTGGGTCGGGTGATGTTTTGGCAGTCAGTAGGTGTAGGGCGACTACGATTGAAACGGTGATTGAGGATATTGTGAG
++
+FFEGGCG?ABFBDFGFGGBBGFEG?#DA?9GDGBCCGFEF=DBF#FDG>FEGCD#EA'BF==DGD6#3A@B5?GC#F.G:,DFGCEFF?:5;:A7#C#F=
+@SimSeq_11/66/1
+TGCTCGAACCCATAAGAAACTTATGGTTAGTAGGAGAGCCTTGCTTATTAGGGCAATGGTGAATAGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGA
++
+GG;EBGGEGEDCDGGFDED?,DDG?GDGEFGFFD@G;EA@EAEGG)GCDA#CEF7ADAGB=EBEGF#A?G?<ACCCFEDD?#F:B>E#FAA##9G###?>
+@SimSeq_12/241/1
+ATGCCGGATAGAGTCCTGCAAACCTTAAATCAAGAAATGGGGGGTTGTTTACTCCCATTTAGGGCTTTGAAGGCCCTCGGCTTGGAATTTACACCTAATT
++
+DGDDE8EGGGGGDGGEEDDE4EDEDCDF?EDBGF?=-AGGB:GFCBGE=?AFBGFAD9B@DAE:F0@>D@C=B=CGC=G#D7??FADBCC#:#:#>DB3E
+@SimSeq_13/221/1
+TACCTGCTTTTATCCTTTTACTATCTCTACTTCATATAACCGCCCACCCGGTCGGTTTTAAAAAAATGATAATTAAACTAGCATTTTTCACCAGCCTCCC
++
+G=DG;DGE<5A>GEGGDAEDFEGCBEEFGF?GF=CFCGAF=CFEEAG>@FFG?=GGEF7FCGE#A@B?E=FB@AB,C5AD@G,@BB@)F1D#F##GB#C#
+@SimSeq_14/154/1
+CACTCAATATTTAACCGAGAGAGATCCGCGCAGGAACTGCTAATTCCTAGCCCCCAGGACTAACAGCCTGGCCCTCTCGTCGTGGGCTCGGTAAGTGAAG
++
+GDEBAFE=GBDG=G@GGGE?DE?FCGGDEG:GAC??BGDBEF=BGC:?FEEFAFB?-#CDFCDECEGA=E;FCEBEG#BEGDGDCEDAA###E5;:###E
+@SimSeq_15/76/1
+GGTTGTTAGTCAAGGTTCTGGGTTTAGTTGTGGCATGGTCACTAAGGGGGAGGGGGTAATACTAGTCCCCTAATCCAGATCGGAAGAGCGGTTCAGCAGG
++
+GEGDGGEDA=GFG@=FGGGG=GDBFGGF@EAEGEEG:GFDGDBGCGDEEEDDGGG7CF@:@A=AA1@A?EAEECFEEDDCFDBEDEDBD###F>=BA@E#
+@SimSeq_16/55/1
+TTTATGGTTCAGGCACGGATCCTAAGTCATTGGTGGTAGTCCAAACATTGATATTAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAA
++
+ADGFBFCCF?DGDEGDFDDFDGEGGE@CDFD=DEBFC-G:EGBF?B+EGBDAGEAE?DEFCBF'?=@E5E=FGBE;=AFECA15FDBA#EE,:5B=#DEB
+@SimSeq_17/122/1
+CCCCAATAACAGGCCTCATCTCCTGAACAGACACCCTACTATGACTATCAATTCTACTAGCTTTCCGAGTAAAAATCCCCCTCTATGGTTTACATCTATG
++
+GGDGCEGGFGGDEGGCGCGDAGC7GFBDAC=GCEDD;AEGDG?2A>E=G*CE>D:GDG:EG?D->A#>DE1BBE2DEBDCDBEF8?F6??D#C:CE##FE
+@SimSeq_18/188/1
+TTTGTAGTTGTATTCGGTAGTGGTTTGTTAATTATTGAGGGTGGAAGTTTTATGCCTTTAGTGGTGTTATTAGTTTATTTAGGGGGGTTATTGGTGGTGT
++
+FG=DFDFGGGGFGGE=DGD=BGDEGEFG;FB=C=EEAFGCEA5EBDGEGBDF?AEAEAFC>BAE:#EG=BDG##E=GG@#CEFA;?#DCE@-#BC6D###
+@SimSeq_19/46/1
+ANACCACAAACGCCAATATGCGTAACAAACCCCAGCAAAGAACCCCAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAAAAAA
++
+D#DGFEF>GDG3GEF?EEGCGFGGGGD?EGGG:GGGDGG:EECFFG-3ECDD@E5>?#F@@DA#F8@:;:GBG9CEE9C>DEDB7DCE:#?:EEF#55A#
+@SimSeq_1a/16/1
+GTGATATAAAGGAGGTAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+DAGG>GGGAECFDEFBFDBE?GBDEFGCGGGE5CBCGBGEB?DDAG?A=BGA#0=E?GBDFF#CG>E??A=?;C=CAE=?#DE;?#DF>5EBF?B#E##<
+@SimSeq_1b/116/1
+TGGAGGATACAGATGAAAATGCTAGAGTATCGCTTGATGAAAAGTGCATTATTAAGAAGAGTCTTGTTAGAATCTGAATTAATAGGGTTAGGCCTAGTAG
++
+7B9BG;6GDGGGFFGBGD==DGGGAEGEBGDG@@FFDFEGFE?;?EBA#?>FED4AB:DD?DE0B0F@B@FEE;EE?E??C:F5EA#=9ABE7C#GB-##
+@SimSeq_1c/138/1
+TTGTGTTTGCTTTTTGTGTTGGGTTTACTGATGATCCATTTGGGGGGTTTTGAGGAGTGGGGGTGTCTAAGTGGGTCGTATTTTTTTGATGGGCGGGGTT
++
+E<GFCDGGFDG2@DGE;FGFFEE,:GGGDGGDGBGEFD?GG==@EFE??EA>ECFDED@?EDFB??FEBFAF>A?,:DGA:#,FC#G;#C??A##:E>#D
+@SimSeq_1d/195/1
+TTGGGCAGTCAGTAGGTTTAGGGCGACTACGATTGAAACGGTGATTGAGGATATTGTGAGTATGATAAATAGGTTAATTGCTTTTCCACGGGTGGGATAA
++
+FC5GFGGCDG:EG6EFED=?:FCD@GGEDBF>DGEFDFDDFE?3AACCGCEF?DDDGADBE7CADB?BBB@B???E#BF@>#GFE:C#FAD@B#BDB#C#
+@SimSeq_1e/0/1
+AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAA
++
+AEEGD=GFBFG=FADFGDEGGEB8@CBGFEFBGGGEGAGAFGDD=DAFFBEDEBDF7EBGA?GGB@?EBA#DEF@D.B<ECDAC@B??###F-##@2#D?
+@SimSeq_1f/145/1
+ACTGCCCTACACTTCCTCCTTCCATTCGCCCTATTGGCTTCACTCATCACCCACCTGATCTTCCTCCATGAACGAGGATCATTTAACCCCCTAGGAATTA
++
+?GE?6AGFDDF8A?GDGFDEDBBEEF;EEDCF?BFFDD7#EGGADF>GDBDDDFG:CFGC7C?DEG@E6@GBABF<3:EBE#EAC=#BCA##B#CG;##A
+@SimSeq_20/104/1
+TTAGCATTGTAGCAGGTTTAGGTTTTTGAGGCTCGCCGTATTATGAGTTCGAGCAGAGGCGACTAATAAGGCAAGGCCAACTCCTGCTTGACAAGCGGAT
++
+DGCEBCD-GGGECEEF?DACFEEADGDGAG7AEFFGC?EDECG0A?:#-DG7GGDEE>??BFC==*GE@:>=AD#C@@F?GA;@CAE?A##BAFEB##:C
+@SimSeq_21/50/1
+AGAAACTTATGGTTAGTAGGAGAGCCTTGCTTATTAGGGCAATGGTGAATAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAA
++
+EE/DDGGFFEG=GG=EBCE9EB:EEABBD?FD;G::FC@#GE?GEG?D=GCA?FAECGE6AAE-D?A0DF:5>C<A#EACFBE#DDDD#D>E5>#DEB##
+@SimSeq_22/0/1
+AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+@GFGGDFDGGFD?EEGGGGBCEDDCCDFF@GB;EEGGG7DD5EGFAG6EDGEAFGAABCG.B:EBEGE:F5@-D?6C2=F:#GCC#6@5=E?=D=E#A##
+@SimSeq_23/196/1
+TAAATTTTACCTTCTTCCCACAACACTTCCTAGGACTATCTGGGATACCTCGACGATACTCGGACTACCCAGACGCATACACCCTCTGAAACCGAACATC
++
+EEDG@CGGFGDGFDDAGGFDGDCGFDCAGE<AGGEGDGBG@G4BDEE-?EDG?E9C>E@?CDGG,BEBGFGC=#A@C>D#ADDG5C9E#,#BA#56@=:A
+@SimSeq_24/0/1
+ATATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+F3GFGG;:CCGGGDAGE@AGD?AC>0E@FE@DFG=GBEDFFGEGFGGEEE#FBF@G3GEEDB#B:DE?A><5:D=EB=BFGDAG@GEBAG#5#ADDF#D5
+@SimSeq_25/224/1
+CTAAACAGAATAATATAGAAGATGTTATTCCATGGGCAATCATTAGGATTATTGACCCTATCGGGGTTAGTTGGTTTCGGGTGAGAATTGCAGCTGTTAC
++
+G?EGDEGGFDFDFFEGFDABFGBCF5G=G>FF<F5DD7BBGG?>FG<F?EFBEEAFDE#EGGCECDC)#DG#E@5D?E7F>#DE:>#DF##=BB?=#G@#
+@SimSeq_26/97/1
+GATAACTGCAACCATGGAAATTAAGGATCCAATTGATGATGTTAGGTTTCAGAGGGTGTATGCGTCTGGGTAGTCCGAGTATCGTCGAGGTATCCCAAGA
++
+>GGAGFGBEDFGGGDFGFGA*GDFD=DGDEDCGG>FFEE5E=DDGCCCE?GDE3=CGDFGGC?>#DEFCE8DFEED#BFCBD?DA#D#A#AA#FB#9#?E
+@SimSeq_27/144/1
+ATAGGTGATTAAAGAAGCTAATAATTTTTAGGTCTGAATCTATATATAATTCGGTGAATTCTATAATTGATCATGTGACAAACAGTGCTGTGGGGACGAA
++
+E;GGA?GDD?GEGFGDEGAGGAB:CE@FE:BEFEFFF8GGDGG;?G@D=G?G??6AF#AD#FB??=#=EF3;#E@E>:DB?B?;F#D#?:C#E#E??C#?
+@SimSeq_28/124/1
+TAATTATGGAATTTGCTGGGGTGAAGTTTTCAGGGTCCCCTAATAGGGCTGGTAGGTAGAGAGCTAAGATGAGTAGTGAGGAGGCAGCTAGTGCTGCTCC
++
+D9AFG:D=GGGCG@AGGBGFCEGD?GEEEGFE@E?ECBGEECFDBFEF;DFE:AB@4?FEEEAFGAE::>5DCEEEA:D?C@#G@GCE#BCAD;E8=?D#
+@SimSeq_29/224/1
+TGATGAGTGAAGCCAATAGGGCGAATGGAAGGAGGAAGTGTAGGGCAGTGAAGCGTGTAAGTGTTGCGTTGTCAACAGAGGGGCCGCCTCAAATTCATGG
++
+EGGGCGEGDDCGGGGDACDA;GFEG:FCGGDEC=:GFF>BAEDFEEGF;CE>E@CE>GCB=CA#:C>F(A;B85B7CCE=BA6##A>>E@:5@B#BDE#B
+@SimSeq_2a/120/1
+CGAGCGGAGATGGTATGGGGAGGGGGGACCACATGGCGAGAGCAAGTATTAAGGCAGCTGTTGGGGCCAGGATGAAAAGGGTAGGGGTGGCAAGCAGGGG
++
+E7GFGDEGB;CDGGFFDEDFAGEDEG>BFDFGE=BEGGCG>?FDBCFADGD#9AB@EEDGFBAG:1DD:@BGAB>5BD=E5#=@#CCB#A?##7=?E###
+@SimSeq_2b/140/1
+AAGTTGCTTTTTCTGCGAGGAGTTGGTTGATTGTTAATCATTTTGGTATAAAGCCGGCTAGGGGTGGGAGGCCGGATAGTGATAGGAGGGAAATTATCGG
++
+GE-GFGGGGGEFFEF=CG=FACEEEDFGE7EG@BC#EGDBAEA?FGCEC>4-C;G>ED@#9E@DG:DD@>CE??CEA:65@C#E##5AE)G<AE##:##=
+@SimSeq_2c/0/1
+AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA
++
+DGF=D>DCGGGGDDFGG??GFCGGEE??FEB=DFG??EGDF>DDDA?.GFEEG3AEDC@GEC=?C:EE=?BC?F#1ED.DE=D695EGBFE;.#E;BA#>
+@SimSeq_2d/200/1
+CAAGCCGTAGTTGCTGCTTGACTGCTATAGACTACGTGGGAGGTTCGGATTAGCAGGAAAATGCCTGCTACTACTATGGTGCTTGAGTGGAGTAGAGCTG
++
+G?F=EGBEEDDDGFF=GADDEGGFGEB=G9BGFDGCGFBDFG?BG=?DC=3:AGDG#.BD<DCBGG>9CEE@F>6EF>ADAFFC5D@F@ABCB>##<A:G
+@SimSeq_2e/53/1
+CTCGCTGCTATATCATGAATGATCCTAAACAACATCAGTCTGGACATCCAAGAAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAA
++
+<GGG@GFABBDFGGFDGFFEEEEEG5ED=FBGDEDEGCG=?GD5EGD?G:ACF??@BAC:EFGF>F4>##CB5B:#2A?=;?=3B6C;@@#AD:>@5#B#
+@SimSeq_2f/212/1
+ACTATCTGGGATACCTCGACGATACTCGGACTACCCAGACGCATACACCCTCTGAAACCTAACATCATCAATTGGATCCTTAATTTCCATGGTTGCAGTT
++
+G6DEEGGDFDD98GEGFF5?AFEF?CGDEGCB=EFFACCAAGGADFGEE1CFD=FFGEGBGDDC@:G#G:#BE##7#DG#CAD#?DC#G@@A6>B#BFC#
+@SimSeq_30/65/1
+GCGCTGCGAGCTTGGCTGTGTTCGATATGGTTAGTTGGGGGGTGTTGGATGGTAATATAGAGGATAGATCGGAAGAGCGGTTCGGCAGGAATGCCGAGAC
++
+G)DGGEBEGGGGGGDEEEBGBGFGAECE7GEG'EFGG:5AAA>C5FD:?FD<AGFEG:EF=GEFF4=ECD@#AFA;#GDA#?6#DD?>DB>EE?=#F?##
+@SimSeq_31/205/1
+ATTTCTTTTAGCCTAGAGAGTATTCTTGTTTAGTAATTGCTTTCATTAGTGTGGTTGATAGTAGGAGAGTGGTGGTCGCTATGGTGAGGAGGTTGATGGT
++
+DFFFFGEFDEA?CGFFGEF;EGFGGDEFAEEGDEG=FE9G=EGGEGF9=CCG=G?DF#ECEFD?CEE@35B#CG?AG=B5F<CE>=9#C:#F#>DFAAA#
+@SimSeq_32/111/1
+TTCACTGTATTCTACATTAAATCCGGATACTAGTTCCGATTCTCCTTCTGTTAAGTCAAAGGGGGCGCGGTTTGTTTCTGCTAGTGTGGAAGTCTACCAT
++
+D7GGD@GGGFCFECGGGEBEE-GDACDBCF1EDGGGE<5G:E=?F)A?AGEED@BEABB=>8B==5:>C=,?@?E:BE-D2F?C6BDDF6F?C#:#BG?#
+@SimSeq_33/123/1
+GTCCCCTCTGTTGACAACGCAACACTTACACGCTTCACTGCCCTACACTTCCTCCTTCCATTCGCCCTATTGGCTTCACTCATCACCCACCTGATCTTCC
++
+B8EGCDFDGFBEEGCEGBEDE>?EGBEFFDGF45?FAGA?G,G?G-DEECEF>=ECEDECGAD#GAEFF?5EDC;?=GC>?ABFB?E9#CF*#5D##G#B
+@SimSeq_34/23/1
+TAATAGGGTTAGGCCTAGTAGTGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAT
++
+FEF3DDGEFEFDFDGDBDFCGFGBFEGDGGADFCDEEAGDD9GGGBEGB>CCFCEEG,BFG5GD#5BEDCFDADE=AD##G#FBF5AE@)E9B###-###
+@SimSeq_35/203/1
+TCGTAGTCGCCCTAAACCTACTGACTGCCAAAACATCACCCGACCCAGAAAAATTATCCCCTTACGAATGTGGATTCGACCCCCTCGGCTCTGCTCGCTT
++
+F-,F6DFGDF7GEFGDF?D;GCEGCGBGG7B==D=G:FGGDE<GFFBAFEG?E?EEEFDBCAF#EGABEEAC<=*>G#D,DCFEEE##=A;=DEECCD##
+@SimSeq_36/0/1
+AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAATAAAAAAA
++
+FG:FGFEEGEGGGG??EGEFDEFDD?GFGF=G>GGFEEFFE-EBGEED5E<EAEEEEDG?E5FB8D5=B9=EA4DE#CC@DC#:#=>AA2?G#B###BE#
+@SimSeq_37/282/1
+CTTCTGAGTACCAGAAGTTCTCCAAGGAATATCCACAACTGCCGCAAGCTTCCTATTAACCTGACAAAAACTAGGACCATTAATTATACTATTCCTAATT
++
+FD=E?F=G9GFGGFEEG=BC=GEEBDDAGBFDFG=GGDGCDABECGC*GCGG#B>D:CGDF>#EE5G4DBBC94CCE8FE?*#DAFEFC5/D<@#5BB##
+@SimSeq_38/212/1
+GCCAGCGCTTTTCCTTTAGCCACGGGAGTGTGGTGAGGTTTGGTCTTGTTGGGATGGAGGGACTTAGGGGTAACATAGGTGGGTTCAACTATTTTGTTCT
++
+DGGEFA:GCGE:DGBGEDAFGEGE@?GDEG+>;BCEDFE>EGEBGDGACCEFGBF=6?@DBCFF=#EDCE1F::<62D>#2#?6EEE?EEA?AC#BB?DC
+@SimSeq_39/149/1
+AGACCAAACCTCACCACCCTCCCGTGGCTAAAGGAAAAGCGCTGGCCTTGTAAGACCGAAGTGGACGGAACCAACCCTCCCGTGAGTACACCAGCACCCT
++
+FGEBEE==G?:GG>FGCFEDEFACGEDEEADFF5FE)D5F;GFDFEF,EGEBG@EE,AADGGE5B>GF:DEC::E?EC5G##36BGD@#7=?#@)#,+ED
+@SimSeq_3a/195/1
+ATCGGAACTAGTATCCGGATTTAATGTAGAATACAGTGCAAGCCCTTTCGCACTTTTTTTCCTAGCTGAATATGCCAACATTAGATTAATAAATACACTC
++
+FCGG?D-DEFFCEG?EDEGG??FGFE>DGDGEDFBFG4:EEEGGGGGDGGGFEBECDDEF%DA9?GAGF=CB#:13?BEA;C#-ED=A##CC:#=D#A#1
+@SimSeq_3b/93/1
+TCCCTCGTATTTTACATAATCTTCGCCCTATTATTCCCTAAACTATACTACCCAAACACCTCAGACGTTCAAGAAGTAGAAGTAATCTGAACCAGATCGG
++
+FFF,FGGGFDE?FDGDAGCDAGCF1D?DCDGFEF;B8GBDBG?DBG=?FEEAGFC5:F'D?FBEBE.?:D-#EC??@?#=#GDD#:C?E?D?#A:#D#A#
+@SimSeq_3c/122/1
+TTGATAGTTTTTGGCTCATTCGCAGGGTTGTGGTTGGGAAGAAGTGGTGGAATAGGTGGTTGAAGTAGGTTAGTTTAGTTAGGAAGGGCGGTTGGGTGTC
++
+GGGG@AD>CD<?:G?GGGEAGFGGG@FBE:GGBBED=GFEEGA>E?AD<@E>=CF?5#D?DF@B?#B>:='C?B#;EE:G#>B9AE#5AA;?EF5##@1C
diff --git a/tools/seqprep/test-data/input2.fq b/tools/seqprep/test-data/input2.fq
new file mode 100644
index 00000000000..8c02a2322ca
--- /dev/null
+++ b/tools/seqprep/test-data/input2.fq
@@ -0,0 +1,240 @@
+@SimSeq_1/229/2
+GGACTAGTATTACCCCCTCCCCCTTAGTGACCATGCCAAAACTAAACCCAGAACCTTGACTAACAACCTTCCTAATCGTTTGAATCTCCCTTATTGTTAT
++
+BECAFFGCG#5AFGEBB5EBD@ED:=FF?=:GGCD:G?-:AEECECEGABF57F-FFEAFF#EEEAC=A5CEDDDCA#-A#@C=#@?##E#A=@E#>#BD
+@SimSeq_2/49/2
+ATTTAGGGCTTTGAAGGCCCTCGGCTTGGAATTTAAACCTAATTTCTTTAGATCGGAAGAGCGTCGTGTAGGGACGGAGTGTAAAAAAAAAAAAAAAAAA
++
+=AFGG2=CFE6FG:?GEGGADBECGFEEFC>BB96E>5>DDB55=D?:-A=CDFGC4DDCAFA?G#C=#FCD8?#6AFF,EDA#BA##5;D6C#/#-A-A
+@SimSeq_3/149/2
+GGTTGTTGATATTTTGTCTAGTGTTAACAGTGTAGCGGAGATGGTGGTGGAGTAGATGTAGAAGGTTAGGATGGCTAGTGATGGTGGGTATTTAATAACT
++
+GFGEBB=EB@FCDEDGFC#FGD5GGCGGF<BBFFAG?:ECD@BCE:BD9@??B-DADGG7DABADED###:#ABC#ECB?B#F#DF#E##69@8##-#,B
+@SimSeq_4/197/2
+TTACAAATTGGATTTTAGTTCATGTTGGGTGAAGGGTAAATCCTGTAAAGAGTGGGAATCAGTGGGTGAATCCGCTCATGATAGCGAAGACTGCTCCTAT
++
+DFGGGDGF6EGDG;BFB?EEGGG>=E:GBGDGB=G.C?GEDCF#E:E5CB#DBGFDE>CFFC=F7D?8ED=DDCE#9BC@B;#B8#A2;#AECE??C@#E
+@SimSeq_5/40/2
+GCCGCAATACCACCATGCTCCATCCTCCTCTGAGAGGGGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTATAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+GBCEGF:CE0D5FGED7FCAFCBFCG;EAFA#A##FDDCG:8GFADCBCAEDFC#EDFGEDCEDGFDC;D?-D?B?FA7AD#C5#7CA#>###?A;;###
+@SimSeq_6/190/2
+GCTAAAAGAAATTAGGTTTAAATTCCAAGCCGAGGGCCTTCAAAGACCTAAATGGGAGTAAACAACCCCCCATTTCTTGATTTAAGGTTTGCAGGACTCT
++
+GDF=E:EEB=;A>EAEGE@FCGGAGFDEGEGE#:DDGF?BC/DEC#F??=GDD#FDE9@1FGE?EFCDGAGA#EDAB=7FED59=AE+#9##C57>A#B#
+@SimSeq_7/178/2
+ATAGGAAGTACCATTCGGGTTTGATGTGTGTTGGGGTAATTATGGAATTTGCTGGGGTGAAGTTTTCAGGGTCCCCTAATAGGGCTGGTAGGTAGAGGGC
++
+DDEGGGG?D>G@?:GEF>GCGEG=FE;D@GFFE=EC5>=A:GAB?GA?E@D?E7?BDDG:GEA#CGB@;7AEB>;DBCC#CEA2B@:CB#>C##BC###@
+@SimSeq_8/18/2
+ATAAGGGGAGGGAGGCTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAA
++
+AFDG2D?EG?E;?FDG4EFGGD:EEABFEFG??GDEE3G0#DEFE?CDGBGCCFFF,#GBBEG:?C#AF;?GG?E5C>#AGD-3###4#E#A#>#DB?/:
+@SimSeq_9/103/2
+CCAGCCATTGTCCTTATCTCAATTGCCCTACCATCACTACGCACCCTATACCTCATAGACGAAACCAATAACCCCTGCCTGACTATTAAAGTAAGCGGAC
++
+FEG?GGAG:GEAGEF;GDGEG?:EAGB#EAEEG?>#EC57C:F:4FGC-#<EFEAGGD#EEE8GGGFCA-9A:AG5FD'DAGB5A#@G4AEB#CA<#>#:
+@SimSeq_a/334/2
+CCAATGGATGGGATTGCCCATGAGTGTAGTACATCTGCTGCTGTAATTAGTACTCGGATGGTTGAGTTAGTTGGGGTGATTAGGCGGTGGTCAACTTCGA
++
+F:CBBDG9?@AGDE<FEEG?GCAD#EDE5FF5FF#G&BDEGDGD>?C:>CCFF;FADGGEDC??B-CEBBDBBC#:#0DDB##+E#?5#AFB:D?#####
+@SimSeq_b/247/2
+TCTGAGATCTGCGGGGCAAACCACAGCTTCATACCTATCACCATAGAAACCATCCCACTAAACCACTTCCAACTCTGATTAGAATATTCTATTCTCTCCT
++
+DGGGED6BGDGGB=FFAEDGFDGEG056AGGFECECGDG8FD:DFFG=FDBD-BDEB>E>AF;##GCC?GB5CDG7:E#A#;#A#@?@C###GA?G#?D#
+@SimSeq_c/0/2
+ATATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+FFGFG=G:GE=C86GFB:D?GGF?=E-AGG:DE;EG*EEF?G.DGBCD6CGFCD2#=GECE=?F;AEE#5;GD5>8DE7#A;E,=5D5@###C#5#FF#C
+@SimSeq_d/127/2
+TAATTAAACTAGCATTTTTCACAAGCCTCCCTCCCCTTATTTTATTAACTTACAACAACATAGTTGCCCTCTCATTCACTTGACATTGACTCTGCATAGG
++
+DBGFFBABGGDGEEAEE?FBADGC:DFGBCE?BEDAD@CF7EEBC=>A?F5:-5EBEBFDCGGE;#?:?CB=G=3'AD<::7AD?E7E:=*C###FDE##
+@SimSeq_e/84/2
+GGGAGCGGTTGATGAGTTTAATGATTGGGTGGGATTTTCGTAGTTGGTGGGTCATGGGTTTTTATAGTTGAAATACAACAGGGGAGATCGGAAGAGCGTC
++
+CEFEEEGEFFDGEGE9GB,AFDE?C>@DDEDFGAFGDGGBED:G)E4E?C>D(EEF#F=GC9D#E>===ECD;###:GC#F<C#?<B######B###=B#
+@SimSeq_f/64/2
+ACAGGCGTTAATATAAGAGGTGTTTAGTGCTTCAATAATAGCGTCTTTGGAAAAGAATCCTGAGAGATCGTAAGAGCGTCGTGTAGGGAAGGAGCGTAAA
++
+;GDGEGEGC9BGGEGEEGE-ADDAGEFCG=A9A;G;FFFDEE<AFABEFCG@:B=@7=EFC:A??DEGGD#:>=CAGE##EABF>##EBC##A4##C4;>
+@SimSeq_10/154/2
+CACTAGACCCCCAATTATCCCACCAGGGGAAAAGCAATTAACCTATTTATCATACTCACAATATCCTCAATCACCGTTTCAATCGTAGTCGCCCTAAAGC
++
+DFGAFDGGE9=?;:BB>B>:BCCB?DEFD-G?FB@=E9GG:E;E5B)==DEC-GDG9GAG6F;CE:57#A?::DE,EB>BF<ABC=##;B#DC##?##+C
+@SimSeq_11/66/2
+CTATTCACCATTGCCCTAATAAGCAAGGCTCTCCTACTAACCATAAGTTTCTTATGGGTTCGAGCAAGATCGGACGAGCGTCGTGTAGGGAAAGCGTTTA
++
+EEGAEFGFF*GGB;D;GA6B@GFCCEF?EDECGG4EB7?EED#EAAA?<B>2DBC=FA=@BDC9E=BG=E:DCB#GDEA?CD?##C#?5##E#:#7F#@=
+@SimSeq_12/241/2
+ACACAACCCGCCTCTGACGAAAATCTACCCCCCAGAGTAACTTTACCATCAACCTCCTCACCATAGCGACCACCACTCTCCGACTATCAACGACACTACT
++
+FA=DEDGAGGGG=GCFGGGEDF:CG3GCEF@GBGDAG?G6=FEF=GBG?G5@#GEABDDD-@E;#GA9AF=A#F#?AE#:E*?BED8?DE#?#D=##A#C
+@SimSeq_13/221/2
+GAAGAAGATTGAGAAGGTGTCGAGTTTAAGGCTTAAGTAGATGGGGCAGGTTCCTATGCTGAGTCAATGTCAAGTGAATGAGAGGGGAACTATGGTGTTG
++
+FBGGEGGEGDCAEADD?EE=EFGBEGGFFE@G?EGEDGEFGC3BDECBB#CD?FED=D55#F#FA6@<@BFDD@;ECB:?#D:###C#5A###=#@##A#
+@SimSeq_14/154/2
+GTAAGGGGAAGTAGTCTCCTATTTTTAGGTTTACATTCTAATGTTTTGTTTAAACTATACTTACCGAGCCCACGACGAGAGGGCCAGGCTGGTAGTCCTG
++
+#<GGAD#DFGA>=GFGGGGAEGB5DEGEDE*6CDE'EADGG?CAGDF=D54G-<CDDCFECEFGGDA#EE#6=FGEG##-D#5G##A#>FA#B5###B?#
+@SimSeq_15/76/2
+GGATTAGGGGACTAGTATTACCCCCTCCCCCTTAGTGACCATGCCACAACTAAACCCAGAACCTTGACTAACAACCAGATCGGAACTGCGTCGTGTAGGC
++
+DC?D@EGFDGGGCAGDAAGAD;DFGBABDBCDB>FCFFDAGB;FEB=F#,DFD5CF-ECEFF>?G#C#@GGEEGD#-#B?D?;<-#1BG7?59####D?#
+@SimSeq_16/55/2
+AATATCAATGTTTGGACTACCACCAATGACTTAGGATCCGTGCCTGAACCATAAAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAACAA
++
+EFGGGGEC:GFGFG-BGAFDAGG=G>C9E@GEGAEABCECAAD76CFDAC:FC?5GE??FC=EBCG#ADDG=:FAFE=BBAB6A0;#D#B:F:#><D=#A
+@SimSeq_17/122/2
+TTCTACATGAGCCTTGGGGAGTCATAGATGTAAACCATAGAGGGGGAGTTTTACTAGGAAAGCTAGTAGAATTGATAGCCATAGTAGGGTGTCTGTTCAG
++
+GGFEG3GE>DEBG;GDGCEGDFE=C?CG:;GABEAG?#BF<7=FG5.-9>DA?=AE<7FE###?=#EED:=GF#EGF##2>C:F4F?EE=B#E=#CB###
+@SimSeq_18/188/2
+GCCCATCAAAAAAATACGACCCACTTAGACACCCCCACTCCTCAAAACCCCCCAAATGGATCATCAGTAAACCCAACACAAAAAGCAAACACCACCAAGA
++
+FGG2CDGC5GGGGEGF6?DGGG:8EEFE>4CBFFDE>3BFD=E=?B>@DC?E4;G(/F#@>G;:04D#E>:A>E=?#FFBDBB?-#8D#AE;#?#=###C
+@SimSeq_19/46/2
+GTGGTTCTTTGCTGGGGTTTGTTACGCATATTGGCGTTTGTGGTGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAAAAAAAAAAAAAA
++
+>?G4GFD-B7EGGG=D>(=#FFG>E9BGDEFG?DCDEGCGECCD67@7EFEE-FE#?ECAA;:A9GFA#CAF:EA#?DCEAG55#?#.#BC#F5EC4@##
+@SimSeq_1a/16/2
+ACCTCCTTTATATCACAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACA
++
+@GEAEGECGFAGFG:1FAG=GF@FEBG:C5FGDEEBGFGB#?EEFDG5GCF-=GEC#*@GD75DD@BD?;2A7;G@-G#?GF5F?#BB#F#A7EG##B#?
+@SimSeq_1b/116/2
+ATTAAACTTTGGATCACTACTAGGCCTAACCCTATTAATTCAGATTCTAACAGGATTCTTCTTAATAATGCACTTTTCCTCAAGCGATACTCTACCATTT
++
+;E2GFG;;FFGG?:EG<BGE;#C>D-6EEA/7GDD=EA=GDG4E=FF?=?EE:?7GBEE@DG:-E#GA=55>:?E:F5#<>):*#?C#=<#=>B##:5?:
+@SimSeq_1c/138/2
+ACCACAAACGCCAATATGCGTAACAAACCCCAGCAAAGAACCCCGCCCATCAAAAAAATACGACCCACTTAGACACCCCCACTACTCAAAACCCCCTAAA
++
+AGGAFGDGGGGFG;EDGEGCCGDGA@E;=GGEGFB-G=G=DFG:GGE?A:@E:DEDDBD5G#AGF:GD:EBG#F@E>G1F#EF#F#A:>##>A#B#>4##
+@SimSeq_1d/195/2
+TCGTCTGACTTTTCCTCTATATCTCGATCTACTGATGAGGATCGTGCTTTTCTAGTACAAACAATACAAGTGACTTCCAATCACTAGACCCCCAATTATC
++
+F?D8GGGEGFDFGDEF=FE.=EFCEEABC+?FGE=C?DFC'.GBF=GG7F*B#:>BEA5??A?:5#EC==#.2G?DA.A?#EF#1AC#B##=F?EA###A
+@SimSeq_1e/0/2
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+GGGG0DFGGGAEC=<E?DGAEGFAAED?=GBFFDBDDC-3G<F-=55<:ECF=5;D>@#AEDEB?DAED:D:-#DDE#AE:A:=E+8#DA-#.E@#?#8#
+@SimSeq_1f/145/2
+TTATGGTGAAGTAGGGGTGGAATGGGATTTTGTCAGCATTTGGGCTAATTCCTAGGGGGTTAAATGATCCTCGTTCAGGGAGGAAGATCAGGTGGGTGCT
++
+GAED=EGGEFGG<1D=6FAGE;GED)?DGG#EGE<B:GCAEGEE:GB#=E;C5G?#ADBCB@D#BDA-AG5CE:GEF#?EB#/>#####DGC#E+##:#A
+@SimSeq_20/104/2
+CCCTATCCGCTTGTGAAGCAGGAGTTGGCCTTGCCTTATTAGTCGCCTCTGCTCGAACTCATAATACGGCGAGCCTCACAAACCTACACCTGCTACCATG
++
+7FBGGGGFG@E5>GGGDEG5FAG>:DA5GFG?EAE;:GE>E>?F@CG6.D=B,A;#G#AG8A?CDADACCC?C;A#DD.AFBCAB##B-A#DF3#A##??
+@SimSeq_21/50/2
+ATTCACCATTGCCCTAATAAGCAAGGCTCTCCTACTAACCATAAGTTTCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAAAAAAAAAC
++
+GD==GF=GGGADEEFG=D>@BGEBEC:E>D:GAFG#=GCGAF5FFG56G'=G?A=BE@DC#GCEFG?FG>>A:B@>.9#F2#AFFG##ECEB1-#?##3#
+@SimSeq_22/0/2
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAA
++
+FFAFGCEF:EDDDD:<>CF?:B?FG:EC=<AAD#BF:FDG:5EE@ECECF1DF9BE?DE?GE5C@FE>BAEC5?;-=C@#E@##:?##?<=D##B#####
+@SimSeq_23/196/2
+TCGAGTGCTGTCACTTTTCGTTTTGATGTGAATGCTTCTCAGATAATAAATATTAGAAGGATAACTGCAACCATGGAAATTAAGGATCCAATTGATGATG
++
+@GCEDDGFGEE?BGFG?DGADDGG<G#GBDB=>:E?BD:GFGGGDEEGAC#E5AEDEG-:AB5=EF>:2;?:=EDC#B-@CC?C@######-?#B?GE##
+@SimSeq_24/0/2
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAA
++
+FED=?GFBG>3ED=FDFFDGEGFAGC=:G@6FE5EF?EF@=AD#ADAEBFDE/FCE,?;DC-:CDACCD#DE>B5D4A#+.C+C###C>FC##A####D?
+@SimSeq_25/224/2
+CACAATCTACCCCCCAATTTTAGGCCTAGCGCTCTGGGGGGCACTTATGACAAGCCTCATCTGCTTGCGACAAACGGACCTAAAATCCCTAATCGCTGAC
++
+DGD=GEB?EFGDEEGFEBGC<EFBGFGEAFDABDDGCG-D<G=5BGED:CCF:.DEGABFA:EF?D6.6GB75:FF.?>E)E-==:#5#C:A?/B#B#>#
+@SimSeq_26/97/2
+TGGGATACCTCGACGATACTCGGACTACCCAGACGCATACACCCTCTGAAACCTAACATCAGCAATTGGATCCTTACTTTCCATGGTTGCGGTTATCCGA
++
+GFF#@CFG=EGEFBCF5GCDGEEF?=EBAEGEECGGB,5EG#C:DF>FFCEFDCEDE:EGC&=@@*FB<BE7#>=<#:=4#8#=C@E#=##>###AC#FA
+@SimSeq_27/144/2
+GCCCCATCTACTTAAGCCTTAAACTCGACACCTTCTCAATCTTCTTCGTCCCCACAGCACTGTTTGTCACATGATCAATTATAGAATTCACCGAATTAGA
++
+?GGAEGGGAEFGA;GDEGF;GCGDFG?E=D;FBDC8CBC=G:GEA)-?@DGAEAGDD#AG:EEDECEE=5B:#5,#6A=?DCF5E?=#=E#EA##:<##F
+@SimSeq_28/124/2
+TACTCCACCATAAAAGACGCCCTAGGAGCAGCACTAGCTGCCTCCTCACTACTCATCTTAGCTCTCTACCTACCAGCCCTATTAGGGGACCCTGGAACCT
++
+-G6A:@F:?GEG?EDGF?FGAGG8DEEGG<GAAE4FADE9?F?D#GD4;:EGB5E?GGAG#E;DEE?@DDE5<B=C=C#BE#6D?C#=GG@F#G##A##B
+@SimSeq_29/224/2
+TCTACTCCTAATAGCCACAGCATTTATAGGCTATGTTCTCCCATGAGGACAAATATCATTCTGAGGAGCAACCGTAATCACGAATCTACTTTCTGCCACA
++
+GGGGGC6,?@EFGDFF=G6DGBBGBDD-E#EBGFF#ECEGC35G@?DB=G@DGF@,BFAAGB5F-E=F:G=7DFBG=?A;ADA##DB:A#;###=E#C##
+@SimSeq_2a/120/2
+TTACCAAAGAGTTAACCCTTCCCCTGCTTGCCACCCCTACCCTTTTCATCCTGGCCCCAACAGCTGCCTTAATACGTGCTCACGCCATGTGGTCCCCCCT
++
+GGGGGEEFGEACDF-DG:B=?G@DD?FG-DDGBDCFFC@E>B::D::AF/?A;GBB2E:FBAF=9#?F@F#E:>G#@E,##6:C#%:##E#D#E#?#E##
+@SimSeq_2b/140/2
+CATTATTTCTTTTTCAAAATCCCCAATCACCACCACCATCCTGATAATTTCCCTCCTATCACTATCCGGCCTCCCACCCCTAGCCGGGTTTATACCAAAA
++
+GGGG=AFGFFDC?GGFGEGGCCF;=GCED=EEEG=DG?E#ECEGBEDE5?D9:EGF:D=:@GA0E*G2EGCBF@A@ECF?B##A:B5#C=DC#?DF;-##
+@SimSeq_2c/0/2
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+FEEEGGGD>GEGGFGCGBE5DF5F7F>6GFG6D?FGGFEE@E>??FDA8=?ACE?;:,DGF?=FCBFA5?EBA:@E=#+:=#F65@C>#=###7E#:FA#
+@SimSeq_2d/200/2
+ATCCCTGCCATTGGCCTCGTCCTAGCAGCAACTGGAAAATCGGCCCAATTCGGTTTCCACCCATGACTCCCGGCAGCAATAGAAGGCCAGACACCAGTCT
++
+GBG:ED:>=G?G:EEDFGDFFGDBA<EGBED?BE@E:@BFGGG;::9AFGG@=EEGEFGD#:4D2ADCDEEAAFEBGGEC?A==0CEE###A#AD###:#
+@SimSeq_2e/53/2
+TCTTGGATGTCCAGACTGATGTTGTTTAGGATCATTCATGATATAGCAGCGAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCAAAAAAAAAAATA
++
+AFD;G5CBFDGG=F=DEAGFFFGDD6BE6E5E;GGG$B=EFGGFE4?F?G3?GE5GE;6BGG;ADE=:E#DGGG#D)9B@E?D<:#1##D@.##?7#=#D
+@SimSeq_2f/212/2
+GATGAGATGGGGGGCAGTTGTTAAGTCACTCAATGTTGGTTATTGTTATTTCGAGTGCTGTCACTTTTCGTTTTGATGTGAATGCTTCTCAGATAATAAA
++
+G0G:GGFFEFCGGGF,GGF:>DE@?G56G2GE?>DDEBEEG=DEECECF<>CDGA6C6DFGFFE??F9:FC18AE?#E=A?##:#BCCDGE##G>B#B#@
+@SimSeq_30/65/2
+ATCCTCTATATTACCATCCAACACCCCCCAACTAACCATATCGAACACAGCCAAGCTCGCAGCCCAGATCGGCAGAGCGTCGTGTAGGGAAAGAGTGTAA
++
+EDFFGE?GGE:FEDF;=7GFFGBGGDE=FBGFGGB?GEEG4AG=G5>EB#.EFDB:ED:CE<E?=#GEDA:=+#>#:AGDGB-69##A@-F?EGBECE6;
+@SimSeq_31/205/2
+CTATTCTTCTATCTCCGACTATGATACAACTCCTCATCAACTATGCCACCAAGCACTACCAACACAACCCGCCTCTGACGAAAATCTACCCCCCCAAGTA
++
+EDAE6GEFBG#EDDDEEGGEGA=FCCFEGAA=FDFA>EE5EA-EEG=FA?#>@C6CFEGA=?BEDF:8>DE/DE-:C#FBD>?BCED#DA-?AE##5C##
+@SimSeq_32/111/2
+TCAATAACAATATGGTATACTTCCACACTAGCAGAAACAAACCGCGCCCCCTTTGACTTAACAGAAGGAGAATCGGAACTAGTATCCGGATTTAATGTAG
++
+GGFGBBF=C=7AGEA2FECG(BF>8D?(DFEE?:AECG=FAGACE:A7FGGE?>?'#C-FEF7DFEA?A#A6CAD@D#?#?=#:#DB5#CFG##E>#@#7
+@SimSeq_33/123/2
+GTTAAATGATCCCCGTTCATGGAGGAAGATCAGGTGGGTGATGAGTGAAGCCAATAGGGCGAATGGAAGGAGGAAGTGTAGGGCAGTGAAGCGTGTAAGT
++
+DDGFGEFG?G>GAFBAFF=?D:GFAAAF4GA?EEBEC=BGEFCFEAEFD@?E=GB=CDEG=#G=?#D-:?EF;#;@E*A5C@,56#C7?G?#D9####?#
+@SimSeq_34/23/2
+CACTACTAGGCCTAACCCTATTAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAA
++
+?=EGF3EAGFFGFACEG=BFCGFADCFD7>EGA:EGBF@:>*CD:CC??-:EEDE:D=D:GF=D=EE#->C1BE1CG+:##D#:D)#E#C#*@C#?A###
+@SimSeq_35/203/2
+GTTGAGGGTGTGGATGGCTCATGTGAGTGGTAGTAGGATGGCAATTTCAAGGTCAAAAAGCAGGAATAGGATGCCTACTAGAAAGAACCGGATTGATAGG
++
+DEAEEGA-CFDFEGFGFBDA>AFGC>;AGDE2:AEA>FADFE;E=#GE@FCD:C@A5GGGDFFACB5E:C?#FCF=;E5C&@FF9#:CF:###C>F#?#C
+@SimSeq_36/0/2
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAG
++
+DG5F::GBDGCE?DGGEGD9DGD=A6EDBC>:EGEF=ADCA8GAFF:?@DFE:?G5E>5-GD=B?F5E5?.D5-#G?:F,?F4#/#>FD#=-A#B#@###
+@SimSeq_37/282/2
+TAGAAGGTTAGGATGGCTAGTGATGGTGCGTATTTAATAATTACGATAATTCATGCTATTTCGGCAATGGACGATAGTGCTATTAATTTTCGTACTTGAG
++
+EGEBGG?GBFDGGGACGF?F=6AACFC,GEG0EGDE#DGEFD:C=7D1E#DGD1FEGG=6GE#@@DCCCDCE@A2=##EF##C=A8E#A<#:##=#?#B#
+@SimSeq_38/212/2
+ACATGAATCGGAGGCCAACCAGTAAACCCCCCATATATTTTAATTGGCCAAACTGCCTCCCTATTCTACTTCATCATCATCCTAATCCTCATACCAATAG
++
+GDDCEGB==E?DEDEEFAAEAA?EEGCA>FFD-5;D@EF::FC5AE6G?GC?E=AFFEDABEE5EDE#.EBACD#BBAD#F@-#F-###?##:##?EF15
+@SimSeq_39/149/2
+GGCTTTGGGGGCCGAAGGTGCAAAGTTTTGTTTGCTTTCTTGATACCGGAGGGTGCTGGTGTACTCACGGGAGGGTTGGTTGCGTCCACTGCTGTCTTAC
++
+GGEFGA:EFDFD=GBAACGDGGG=G5AD6ECG:G?GEA@CB?A:5EB?A>BEAA?-G:AD5A9=DDB?A=E5AE#FEA5A##EA:D@C??-:D#BA###C
+@SimSeq_3a/195/2
+CTTATGGTTAGTAGGAGAGCCTTGCTTATTAGGGCAATGGTGAATAGTGCTGGGAGGAAGGTGGGGGTTGATGGGCTGAGACACAGGGTGGTGGTCAGTG
++
+G?GGGEGEGAGEGFG=-B8F?C=AEG>E8EA@E#GG=?FDG#D:=EBGE@EECCDEDFFB=;EFAB=:#>FAC##BCD##B#EDG#??G###@###GD>#
+@SimSeq_3b/93/2
+GGTTCAGATTACTTCTACTTCTTGAACGTCTGAGGTGTTTGGGTAGTATAGTTTAGGGAATAATAGGGCGAAGATTATGTAAAATACGAGGGAAGATCGG
++
+EFCFCDECEB=DDAGCE?GGACFGD:3EF?FED>F=AFCBDDEAFDG=GFA43=EF=BDEDGF?F#=EGC@B?#;-AC5=#AE6#?B#E#>#?:?####5
+@SimSeq_3c/122/2
+TAAATTCCCGCCCATTACCAACGACACCCAACCGCCCTTCCTAACTAAACTAACCTACTTCAACCCCCTATTCCACCACTTCTTGCCAACCACAACACTG
++
+-:E?DE>EG>BFFDDGGGBDEE=C:>DDG?FG8#8AA;5CAB?.F@B:AG==FA?C;D0-:=D##-BDEDEAC:F#:?C#GFGG-B>F#*#?C#E##>3#
diff --git a/tools/seqprep/test-data/merged_output.fq.gz b/tools/seqprep/test-data/merged_output.fq.gz
new file mode 100644
index 0000000000000000000000000000000000000000..0db37d1dfca44a3854a4ffeb1dc44abcc85d62f0
GIT binary patch
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z4Zv;O*g}Ip$vvO%I(l!*cUQ-+dm|qEt+udcRjaakN-fu>W)&ioG#fEH@C|i0%@u+!
z0;ea1o-B;KME2@E2?{ib{SBsrYbXVD*w<a?JIh9m4hegB^>a`6k9%{xLuW1dv2kH4
z?%Bu}{<ycolWp`kER%gpOvcftIWjyN6s9X~fTAt}My_@k!J=-l+WyQ$^#Uk~2&d7?
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zm~HZo?%mjCl>sgr4b3CZ4ObaA8rdXmAH7LE!*&c<Z=>Q?l5VxKc^|-cjVHKUB;C@J
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z>U8#TR~?VtB{zE8_Ph;fqoGNkb1`bwY2B7;7qz+;tc-TqH3c!;mKbUY!n(^X+=%9h
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HcmV?d00001


From 88bf66450b38557016c853aff233e2fa227f2b0a Mon Sep 17 00:00:00 2001
From: Albert Ratschinski <128725036+Alby-Git@users.noreply.github.com>
Date: Tue, 16 Jan 2024 14:04:31 +0100
Subject: [PATCH 2/9] Update tools/seqprep/.shed.yml

fixed linting error for shed.

Co-authored-by: paulzierep <paul.zierep@googlemail.com>
---
 tools/seqprep/.shed.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/seqprep/.shed.yml b/tools/seqprep/.shed.yml
index 07cc64e01fa..dff8b7f6751 100644
--- a/tools/seqprep/.shed.yml
+++ b/tools/seqprep/.shed.yml
@@ -6,7 +6,7 @@ long_description: |
     SeqPrep is a program designed to merge paired-end Illumina reads that are overlapping into a single longer read and to trim adapters.
     It is particularly useful for preparing reads for downstream applications like genome assembly and SNP calling.
     The tool works by identifying and merging reads that are overlapping and trimming adapters based on user-defined sequences or default parameters.
-  remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep
 categories:
 - Sequence Analysis
 - RNA

From 0fab6dabf170a124a601c6d320faa9bc2faa4e24 Mon Sep 17 00:00:00 2001
From: Albert <ratschinski.albert@gmail.com>
Date: Tue, 16 Jan 2024 14:30:25 +0100
Subject: [PATCH 3/9] fixed linting error

---
 tools/seqprep/.shed.yml        |   4 +-
 tools/seqprep/seqprepFinal.xml | 301 ---------------------------------
 2 files changed, 2 insertions(+), 303 deletions(-)
 delete mode 100644 tools/seqprep/seqprepFinal.xml

diff --git a/tools/seqprep/.shed.yml b/tools/seqprep/.shed.yml
index 07cc64e01fa..a942c76ef1a 100644
--- a/tools/seqprep/.shed.yml
+++ b/tools/seqprep/.shed.yml
@@ -2,11 +2,11 @@ name: seqprep
 owner: iuc
 description: Tool for merging paired-end Illumina reads and trimming adapters.
 homepage_url: https://github.com/jstjohn/SeqPrep
-long_description: |
+long_description:
     SeqPrep is a program designed to merge paired-end Illumina reads that are overlapping into a single longer read and to trim adapters.
     It is particularly useful for preparing reads for downstream applications like genome assembly and SNP calling.
     The tool works by identifying and merging reads that are overlapping and trimming adapters based on user-defined sequences or default parameters.
-  remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep
 categories:
 - Sequence Analysis
 - RNA
diff --git a/tools/seqprep/seqprepFinal.xml b/tools/seqprep/seqprepFinal.xml
deleted file mode 100644
index 7fa6a844f84..00000000000
--- a/tools/seqprep/seqprepFinal.xml
+++ /dev/null
@@ -1,301 +0,0 @@
-<tool id="seqprep" name="Merging paired-end Illumina reads (SeqPrep)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description>Merge and Trim Adapter Sequences from Paired-End Illumina Reads</description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="biotools"/>
-    <expand macro="requirements"/>
-    <command detect_errors="exit_code"><![CDATA[
-        SeqPrep
-            -f '${input1}'
-            -r '${input2}'
-            -1 '${output1}'
-            -2 '${output2}'
-
-            #if $merge_reads
-                -s '${merged}'
-            #end if
-
-            ## General Arguments ##
-            #if $general_options.first_read_discarded
-                -3 $general_options.first_read_discarded
-            #end if
-            #if $general_options.second_read_discarded
-                -4 $general_options.second_read_discarded
-            #end if
-            #if $general_options.phred64
-                -6 $general_options.phred64
-            #end if
-            #if $general_options.quality_cutoff
-                -q $general_options.quality_cutoff
-            #end if
-            #if $general_options.min_length
-                -L $general_options.min_length
-            #end if
-
-            ## Additional Adapter/Primer Trimming Arguments ##
-
-            #if $trimming_options.adapter_a
-                -A $trimming_options.adapter_a
-            #end if
-            #if $trimming_options.adapter_b
-                -B $trimming_options.adapter_b
-            #end if
-            #if $trimming_options.adapter_overlap
-                -O $trimming_options.adapter_overlap
-            #end if
-            #if $trimming_options.max_mismatch_fraction
-                -M $trimming_options.max_mismatch_fraction
-            #end if
-            #if $trimming_options.min_match_fraction
-                -N $trimming_options.min_match_fraction
-            #end if
-            #if $trimming_options.adapter_bandwidth
-                -b $trimming_options.adapter_bandwidth
-            #end if
-            #if $trimming_options.gap_open
-                -Q $trimming_options.gap_open
-            #end if
-            #if $trimming_options.gap_extend
-                -t $trimming_options.gap_extend
-            #end if
-            #if $trimming_options.gap_end
-                -e $trimming_options.gap_end
-            #end if
-            #if $trimming_options.local_alignment_score
-                -Z $trimming_options.local_alignment_score
-            #end if
-            #if $trimming_options.read_alignment_bandwidth
-                -w $trimming_options.read_alignment_bandwidth
-            #end if
-            #if $trimming_options.read_alignment_gap_open
-                -W $trimming_options.read_alignment_gap_open
-            #end if
-            #if $trimming_options.read_alignment_gap_extend
-                -p $trimming_options.read_alignment_gap_extend
-            #end if
-            #if $trimming_options.read_alignment_gap_end
-                -P $trimming_options.read_alignment_gap_end
-            #end if
-            #if $trimming_options.read_alignment_max_gap_fraction
-                -X $trimming_options.read_alignment_max_gap_fraction
-            #end if
-    ]]></command>
-    <inputs>
-        <param label="First Read Input (FASTQ)" name="input1" type="data" format="fastq" />
-        <param label="Second Read Input (FASTQ)" name="input2" type="data" format="fastq" />
-        <param label="Merge Reads" name="merge_reads" type="boolean" truevalue="true" falsevalue="false" />
-
-        <!-- Section for General Arguments -->
-        <section name="general_options" title="General Arguments (Optional)" expanded="false">
-            <param label="First Read Discarded FASTQ Filename" name="first_read_discarded" argument="-3" type="text" optional="true" help="first read discarded fastq filename" />
-            <param label="Second Read Discarded FASTQ Filename" name="second_read_discarded" argument="-4" type="text" optional="true" help="second read discarded fastq filename" />
-            <param label="Input Sequence is in Phred+64 Format" name="phred64" argument="-6" type="boolean" truevalue="-6" falsevalue="" checked="false" help="Input sequence is in phred+64 rather than phred+33 format, the output will still be phred+33"/>
-            <param label="Quality Score Cutoff" name="quality_cutoff" argument="-q" type="integer" optional="true" value="13" help="Quality score cutoff for mismatches to be counted in overlap" />
-            <param label="Minimum Length of Reads" name="min_length" argument="-L" type="integer" optional="true" value="30" help="Minimum length of a trimmed or merged read to print it" />
-        </section>
-
-        <!-- Section for Additional Adapter/Primer Trimming Arguments -->
-        <section name="trimming_options" title="Additional Adapter/Primer Trimming Arguments" expanded="false">
-            <param name="adapter_a" argument="-A" label="Adapter Sequence A" type="text" optional="true" value="AGATCGGAAGAGCGGTTCAG" help="Forward read primer/adapter sequence to trim as it would appear at the end of a read" />
-            <param name="adapter_b" argument="-B" label="Adapter Sequence B" type="text" optional="true" value="AGATCGGAAGAGCGTCGTGT" help="Reverse read primer/adapter sequence to trim as it would appear at the end of a read" />
-            <param name="adapter_overlap" argument="-O" label="Minimum Overall Base Pair Overlap with Adapter" type="integer" value="10" optional="true" help="minimum overall base pair overlap with adapter sequence to trim" />
-            <param name="max_mismatch_fraction" argument="-M" label="Maximum Fraction of Good Quality Mismatching Bases" type="float" value="0.02" optional="true" help="maximum fraction of good quality mismatching bases for primer/adapter overlap" />
-            <param name="min_match_fraction" argument="-N" label="Minimum Fraction of Matching Bases" type="float" value="0.87" optional="true" help="minimum fraction of matching bases for primer/adapter overlap" />
-            <param name="adapter_bandwidth" argument="-b" label="Adapter Alignment Band-width" type="integer" value="50" optional="true" />
-            <param name="gap_open" argument="-Q" label="Adapter Alignment Gap-Open" type="integer" value="8" optional="true" />
-            <param name="gap_extend" argument="-t" label="Adapter Alignment Gap-Extension" type="integer" value="2" optional="true" />
-            <param name="gap_end" argument="-e" label="Adapter Alignment Gap-End" type="integer" value="2" optional="true" />
-            <param name="local_alignment_score" argument="-Z" label="Minimum Local Alignment Score Cutoff" type="integer" value="26" optional="true" help="Adapter alignment minimum local alignment score cutoff [roughly (2*num_hits) - (num_gaps*gap_open) - (num_gaps*gap_close) - (gap_len*gap_extend) - (2*num_mismatches)]" />
-            <param name="read_alignment_bandwidth" argument="-w" label="Read Alignment Band-width" type="integer" value="50" optional="true" />
-            <param name="read_alignment_gap_open" argument="-W" label="Read Alignment Gap-Open" type="integer" value="26" optional="true" />
-            <param name="read_alignment_gap_extend" argument="-p" label="Read Alignment Gap-Extension" type="integer" value="9" optional="true" />
-            <param name="read_alignment_gap_end" argument="-P" label="Read Alignment Gap-End" type="integer" value="5" optional="true" help="read alignment maximum fraction gap cutoff" />
-            <param name="read_alignment_max_gap_fraction" argument="-X" label="Read Alignment Maximum Fraction Gap Cutoff" type="float" value="0.125" optional="true" />
-        </section>
-    </inputs>
-    <outputs>
-        <data format="fastq.gz" name="output1" label="${tool.name} on ${on_string}: First Read Output">
-            <filter>output_all</filter>
-        </data>
-        <data format="fastq.gz" name="output2" label="${tool.name} on ${on_string}: Second Read Output">
-            <filter>output_all</filter>
-        </data>
-        <data format="fastq.gz" name="merged" label="${tool.name} on ${on_string}: Merged Reads">
-            <filter>merge_reads</filter>
-        </data>
-    </outputs>
-    <tests>
-        <!-- Test default inputs #1 -->
-        <test expect_num_outputs="3">
-            <param name="input1" value="input1.fq" />
-            <param name="input2" value="input2.fq" />
-            <param name="merge_reads" value="true" />
-
-            <!-- Section for General Arguments -->
-            <section name="general_options" >
-                <param name="quality_cutoff" value="13" />
-                <param name="min_length" value="30" />
-            </section>
-
-            <!-- Section for Additional Adapter/Primer Trimming Arguments -->
-            <section name="trimming_options">
-                <param name="adapter_a" value="AGATCGGAAGAGCGGTTCAG" />
-                <param name="adapter_b" value="AGATCGGAAGAGCGTCGTGT" />
-                <param name="adapter_overlap" value="10" /> 
-                <param name="max_mismatch_fraction" value="0.02" />
-                <param name="min_match_fraction" value="0.87" />
-                <param name="adapter_bandwidth" value="50" />
-                <param name="gap_open" value="8" />
-                <param name="gap_extend" value="2" />
-                <param name="gap_end" value="2" />
-                <param name="local_alignment_score" value="26" />
-                <param name="read_alignment_bandwidth" value="50" />
-                <param name="read_alignment_gap_open" value="26" />
-                <param name="read_alignment_gap_extend" value="9" />
-                <param name="read_alignment_gap_end" value="5" />
-                <param name="read_alignment_max_gap_fraction" value="0.125" />
-            </section>
-
-            <!-- Outputs -->
-            <output name="output1" file="output1.fq.gz" />
-            <output name="output2" file="output2.fq.gz" />
-            <output name="merged" file="merged_output.fq.gz" />
-        </test>
-    
-        <!-- Without Merging, Two Outputs #2 -->
-        <test expect_num_outputs="2">
-            <param name="input1" value="input1.fq" />
-            <param name="input2" value="input2.fq" />
-            <param name="merge_reads" value="false" />
-
-            <!-- Section for General Arguments -->
-            <section name="general_options" >
-                <param name="quality_cutoff" value="13" />
-                <param name="min_length" value="30" />
-            </section>  
-
-            <!-- Section for Additional Adapter/Primer Trimming Arguments -->
-            <section name="trimming_options">
-                <param name="adapter_a" value="AGATCGGAAGAGCGGTTCAG" />
-                <param name="adapter_b" value="AGATCGGAAGAGCGTCGTGT" />
-                <param name="adapter_overlap" value="10" /> 
-                <param name="max_mismatch_fraction" value="0.02" />
-                <param name="min_match_fraction" value="0.87" />
-                <param name="adapter_bandwidth" value="50" />
-                <param name="gap_open" value="8" />
-                <param name="gap_extend" value="2" />
-                <param name="gap_end" value="2" />
-                <param name="local_alignment_score" value="26" />
-                <param name="read_alignment_bandwidth" value="50" />
-                <param name="read_alignment_gap_open" value="26" />
-                <param name="read_alignment_gap_extend" value="9" />
-                <param name="read_alignment_gap_end" value="5" />
-                <param name="read_alignment_max_gap_fraction" value="0.125" />
-            </section>
-
-            <!-- Outputs -->
-            <output name="output1" file="outputNoMerge1.fq.gz" />
-            <output name="output2" file="outputNoMerge2.fq.gz" />
-        </test>
-
-        <!-- Test with Empty Input Files #3 -->
-        <test expect_num_outputs="3">
-            <param name="input1" value="empty1.fq" />
-            <param name="input2" value="empty2.fq" />
-            <param name="merge_reads" value="true" />
-
-
-            <!-- Section for General Arguments -->
-            <section name="general_options" >
-                <param name="quality_cutoff" value="13" />
-                <param name="min_length" value="30" />
-            </section>  
-
-            <!-- Section for Additional Adapter/Primer Trimming Arguments -->
-            <section name="trimming_options">
-                <param name="adapter_a" value="AGATCGGAAGAGCGGTTCAG" />
-                <param name="adapter_b" value="AGATCGGAAGAGCGTCGTGT" />
-                <param name="adapter_overlap" value="10" /> 
-                <param name="max_mismatch_fraction" value="0.02" />
-                <param name="min_match_fraction" value="0.87" />
-                <param name="adapter_bandwidth" value="50" />
-                <param name="gap_open" value="8" />
-                <param name="gap_extend" value="2" />
-                <param name="gap_end" value="2" />
-                <param name="local_alignment_score" value="26" />
-                <param name="read_alignment_bandwidth" value="50" />
-                <param name="read_alignment_gap_open" value="26" />
-                <param name="read_alignment_gap_extend" value="9" />
-                <param name="read_alignment_gap_end" value="5" />
-                <param name="read_alignment_max_gap_fraction" value="0.125" />
-            </section>
-
-            <!-- Outputs -->
-            <output name="output1" file="empty_output1.fq.gz" />
-            <output name="output2" file="empty_output2.fq.gz" />
-            <output name="merged" file="empty_merged_output.fq.gz" />
-        </test>
-
-        <!-- Advanced Functional Tests -->
-        <!-- General Arguments Test #4 -->
-        <test expect_num_outputs="2">
-            <param name="input1" value="input1.fq" />
-            <param name="input2" value="input2.fq" />
-            <param name="merge_reads" value="false" />
-
-            <param name="quality_cutoff" value="15" />
-            <param name="min_length" value="25" />
-
-            <!-- Outputs -->
-            <output name="output1" file="output1_general_args.fq.gz" />
-            <output name="output2" file="output2_general_args.fq.gz" />
-        </test>
-
-        <!-- Adapter/Primer Trimming Arguements Test #5 -->
-        <test expect_num_outputs="2">
-            <param name="input1" value="input1.fq" />
-            <param name="input2" value="input2.fq" />
-            <section name="trimming_options">
-                <param name="adapter_a" value="ACTGACTG" />
-                <param name="adapter_b" value="GTGACTGA" />
-                <param name="adapter_overlap" value="12" />
-                <param name="max_mismatch_fraction" value="0.03" />
-                <param name="min_match_fraction" value="0.85" />
-                <param name="adapter_bandwidth" value="55" />
-                <param name="gap_open" value="10" />
-                <param name="gap_extend" value="3" />
-                <param name="gap_end" value="3" />
-                <param name="local_alignment_score" value="28" />
-            </section>
-
-            <!-- Outputs -->
-            <output name="output1" file="output1_adapter_trim.fq.gz" />
-            <output name="output2" file="output2_adapter_trim.fq.gz" />
-        </test>
-    </tests>
-    <help><![CDATA[
-    **SeqPrep**
-    
-    SeqPrep is a versatile tool designed for merging overlapping paired-end Illumina reads into a single, longer read. Additionally, it offers the functionality to trim adapter sequences from reads, making it an needful tool for preprocessing Illumina sequencing data.
-
-    **Usage**
-
-    To utilize SeqPrep, start by selecting your input FASTQ files: one for the first set of reads and another for the second set. SeqPrep provides several options to customize your data processing:
-
-    - **Adapter Sequences:** You can provide specific sequences for adapter trimming if they are known. SeqPrep will remove these sequences from the reads.
-    - **Quality Score Cutoff:** Set a threshold for the quality score. Reads with quality scores below this threshold can be discarded or trimmed.
-    - **Minimum Read Length:** Define the minimum length for reads to be retained after trimming. Reads shorter than this length will be discarded.
-
-    If the merging feature is enabled, SeqPrep will combine overlapping reads into longer sequences, thereby enhancing the data quality for downstream analysis.
-
-    **Outputs**
-
-    SeqPrep generates outputs in gzipped FASTQ format. Depending on your settings, this may include:
-
-    - Individual read files (if they are not fully merged).
-    - A combined read file with merged reads.
-
-    ]]></help>
-    <expand macro="citations"/>
-</tool>
\ No newline at end of file

From 4726c086f04e7ac56a8d9905835e3368b747e2bb Mon Sep 17 00:00:00 2001
From: Albert <ratschinski.albert@gmail.com>
Date: Tue, 16 Jan 2024 16:28:06 +0100
Subject: [PATCH 4/9] Changed categories in shed.yml

---
 tools/seqprep/.shed.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/tools/seqprep/.shed.yml b/tools/seqprep/.shed.yml
index a942c76ef1a..f8336894225 100644
--- a/tools/seqprep/.shed.yml
+++ b/tools/seqprep/.shed.yml
@@ -8,6 +8,5 @@ long_description:
     The tool works by identifying and merging reads that are overlapping and trimming adapters based on user-defined sequences or default parameters.
 remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep
 categories:
-- Sequence Analysis
-- RNA
-- Preprocessing
+- Fastq Manipulation
+- Sequence Analysis 
\ No newline at end of file

From c9d464715b2bdae6468cae2f190a5a8ea513bfe4 Mon Sep 17 00:00:00 2001
From: Albert <ratschinski.albert@gmail.com>
Date: Wed, 17 Jan 2024 15:44:57 +0100
Subject: [PATCH 5/9] Fixed Test No. 5

---
 tools/seqprep/output1_adapter_trim.fq.gz | 0
 tools/seqprep/output2_adapter_trim.fq.gz | 0
 tools/seqprep/seqprep.xml                | 1 +
 3 files changed, 1 insertion(+)
 create mode 100644 tools/seqprep/output1_adapter_trim.fq.gz
 create mode 100644 tools/seqprep/output2_adapter_trim.fq.gz

diff --git a/tools/seqprep/output1_adapter_trim.fq.gz b/tools/seqprep/output1_adapter_trim.fq.gz
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/tools/seqprep/output2_adapter_trim.fq.gz b/tools/seqprep/output2_adapter_trim.fq.gz
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/tools/seqprep/seqprep.xml b/tools/seqprep/seqprep.xml
index d8e4edad15e..a607d70bf0c 100644
--- a/tools/seqprep/seqprep.xml
+++ b/tools/seqprep/seqprep.xml
@@ -281,6 +281,7 @@
         <test expect_num_outputs="2">
             <param name="input1" value="input1.fq" />
             <param name="input2" value="input2.fq" />
+            <param name="merge_reads" value="false" />
             <section name="trimming_options">
                 <param name="adapter_a" value="ACTGACTG" />
                 <param name="adapter_b" value="GTGACTGA" />

From 80b9a4259d392960553d44449a4d71f80b12bf53 Mon Sep 17 00:00:00 2001
From: Albert <ratschinski.albert@gmail.com>
Date: Mon, 22 Jan 2024 13:18:29 +0100
Subject: [PATCH 6/9] Changed minor errors.

---
 tools/seqprep/macros.xml                      |  12 +-
 tools/seqprep/seqprep.xml                     | 215 ++++++++++--------
 tools/seqprep/test-data/input1.fastq.gz       | Bin 0 -> 5968 bytes
 tools/seqprep/test-data/input2.fastq.gz       | Bin 0 -> 6131 bytes
 .../merged_output_from_gzipped.fq.gz          | Bin 0 -> 3132 bytes
 .../test-data/output1_from_gzipped.fq.gz      | Bin 0 -> 2286 bytes
 .../test-data/output2_from_gzipped.fq.gz      | Bin 0 -> 2296 bytes
 7 files changed, 128 insertions(+), 99 deletions(-)
 create mode 100644 tools/seqprep/test-data/input1.fastq.gz
 create mode 100644 tools/seqprep/test-data/input2.fastq.gz
 create mode 100644 tools/seqprep/test-data/merged_output_from_gzipped.fq.gz
 create mode 100644 tools/seqprep/test-data/output1_from_gzipped.fq.gz
 create mode 100644 tools/seqprep/test-data/output2_from_gzipped.fq.gz

diff --git a/tools/seqprep/macros.xml b/tools/seqprep/macros.xml
index 141ca993f68..7cb56039a3e 100644
--- a/tools/seqprep/macros.xml
+++ b/tools/seqprep/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.3.2</token>
-    <token name="@VERSION_SUFFIX@">8</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">seqprep</requirement>
@@ -13,7 +13,15 @@
     </xml>
     <xml name="citations">
         <citations>
-            <citation type="doi">10.1134/S1021443716020175</citation>
+            <citation type="bibtex">
+        @online{seqpre,
+          author = {St John, John},
+          title = {seqprep},
+          year = 2016,
+          url = {https://github.com/jstjohn/SeqPrep},
+          urldate = {2016-10-04}
+        }
+            </citation>
         </citations>
     </xml>
 </macros>
diff --git a/tools/seqprep/seqprep.xml b/tools/seqprep/seqprep.xml
index a607d70bf0c..b7084f4562f 100644
--- a/tools/seqprep/seqprep.xml
+++ b/tools/seqprep/seqprep.xml
@@ -1,4 +1,4 @@
-<tool id="seqprep" name="Merging paired-end Illumina reads (SeqPrep)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="seqprep" name="Merging paired-end Illumina reads (SeqPrep)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <description>Merge and Trim Adapter Sequences from Paired-End Illumina Reads</description>
     <macros>
         <import>macros.xml</import>
@@ -7,100 +7,100 @@
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         SeqPrep
-            -f '${input1}'
-            -r '${input2}'
-            -1 '${output1}'
-            -2 '${output2}'
-
-            #if $merge_reads
-                -s '${merged}'
-            #end if
-
-            ## General Arguments ##
-            #if $general_options.first_read_discarded
-                -3 $general_options.first_read_discarded
-            #end if
-            #if $general_options.second_read_discarded
-                -4 $general_options.second_read_discarded
-            #end if
-            #if $general_options.phred64
-                -6 $general_options.phred64
-            #end if
-            #if $general_options.quality_cutoff
-                -q $general_options.quality_cutoff
-            #end if
-            #if $general_options.min_length
-                -L $general_options.min_length
-            #end if
-
-            ## Additional Adapter/Primer Trimming Arguments ##
-            #if $trimming_options.adapter_a
-                -A $trimming_options.adapter_a
-            #end if
-            #if $trimming_options.adapter_b
-                -B $trimming_options.adapter_b
-            #end if
-            #if $trimming_options.adapter_overlap
-                -O $trimming_options.adapter_overlap
-            #end if
-            #if $trimming_options.max_mismatch_fraction
-                -M $trimming_options.max_mismatch_fraction
-            #end if
-            #if $trimming_options.min_match_fraction
-                -N $trimming_options.min_match_fraction
-            #end if
-            #if $trimming_options.adapter_bandwidth
-                -b $trimming_options.adapter_bandwidth
-            #end if
-            #if $trimming_options.gap_open
-                -Q $trimming_options.gap_open
-            #end if
-            #if $trimming_options.gap_extend
-                -t $trimming_options.gap_extend
-            #end if
-            #if $trimming_options.gap_end
-                -e $trimming_options.gap_end
-            #end if
-            #if $trimming_options.local_alignment_score
-                -Z $trimming_options.local_alignment_score
-            #end if
-            #if $trimming_options.read_alignment_bandwidth
-                -w $trimming_options.read_alignment_bandwidth
-            #end if
-            #if $trimming_options.read_alignment_gap_open
-                -W $trimming_options.read_alignment_gap_open
-            #end if
-            #if $trimming_options.read_alignment_gap_extend
-                -p $trimming_options.read_alignment_gap_extend
-            #end if
-            #if $trimming_options.read_alignment_gap_end
-                -P $trimming_options.read_alignment_gap_end
-            #end if
-            #if $trimming_options.read_alignment_max_gap_fraction
-                -X $trimming_options.read_alignment_max_gap_fraction
-            #end if
-
-            ## Additional Arguments for Merging ##
-            #if $merging_options.maximum_quality_score
-                -y $merging_options.maximum_quality_score
-            #end if
-            #if $merging_options.print_overhang
-                -g $merging_options.print_overhang
-            #end if
-            #if $merging_options.min_base_pair_overlap
-                -o $merging_options.min_base_pair_overlap
-            #end if
-            #if $merging_options.max_mismatch_fraction
-                -m $merging_options.max_mismatch_fraction
-            #end if
-            #if $merging_options.min_match_fraction
-                -n $merging_options.min_match_fraction
-            #end if
+        -f '${input1}'
+        -r '${input2}'
+        -1 '${output1}'
+        -2 '${output2}'
+
+        #if $merge_reads
+            -s '${merged}'
+        #end if
+
+        ## General Arguments ##
+        #if $general_options.first_read_discarded
+            -3 '${general_options.first_read_discarded}'
+        #end if
+        #if $general_options.second_read_discarded
+            -4 '${general_options.second_read_discarded}'
+        #end if
+        #if $general_options.phred64
+            -6 '${general_options.phred64}'
+        #end if
+        #if $general_options.quality_cutoff
+            -q '${general_options.quality_cutoff}'
+        #end if
+        #if $general_options.min_length
+            -L '${general_options.min_length}'
+        #end if
+
+        ## Additional Adapter/Primer Trimming Arguments ##
+        #if $trimming_options.adapter_a
+            -A '${trimming_options.adapter_a}'
+        #end if
+        #if $trimming_options.adapter_b
+            -B '${trimming_options.adapter_b}'
+        #end if
+        #if $trimming_options.adapter_overlap
+            -O '${trimming_options.adapter_overlap}'
+        #end if
+        #if $trimming_options.max_mismatch_fraction
+            -M '${trimming_options.max_mismatch_fraction}'
+        #end if
+        #if $trimming_options.min_match_fraction
+            -N '${trimming_options.min_match_fraction}'
+        #end if
+        #if $trimming_options.adapter_bandwidth
+            -b '${trimming_options.adapter_bandwidth}'
+        #end if
+        #if $trimming_options.gap_open
+            -Q '${trimming_options.gap_open}'
+        #end if
+        #if $trimming_options.gap_extend
+            -t '${trimming_options.gap_extend}'
+        #end if
+        #if $trimming_options.gap_end
+            -e '${trimming_options.gap_end}'
+        #end if
+        #if $trimming_options.local_alignment_score
+            -Z '${trimming_options.local_alignment_score}'
+        #end if
+        #if $trimming_options.read_alignment_bandwidth
+            -w '${trimming_options.read_alignment_bandwidth}'
+        #end if
+        #if $trimming_options.read_alignment_gap_open
+            -W '${trimming_options.read_alignment_gap_open}'
+        #end if
+        #if $trimming_options.read_alignment_gap_extend
+            -p '${trimming_options.read_alignment_gap_extend}'
+        #end if
+        #if $trimming_options.read_alignment_gap_end
+            -P '${trimming_options.read_alignment_gap_end}'
+        #end if
+        #if $trimming_options.read_alignment_max_gap_fraction
+            -X '${trimming_options.read_alignment_max_gap_fraction}'
+        #end if
+
+        ## Additional Arguments for Merging ##
+        #if $merging_options.maximum_quality_score
+            -y '${merging_options.maximum_quality_score}'
+        #end if
+        #if $merging_options.print_overhang
+            -g '${merging_options.print_overhang}'
+        #end if
+        #if $merging_options.min_base_pair_overlap
+            -o '${merging_options.min_base_pair_overlap}'
+        #end if
+        #if $merging_options.max_mismatch_fraction
+            -m '${merging_options.max_mismatch_fraction}'
+        #end if
+        #if $merging_options.min_match_fraction
+            -n '${merging_options.min_match_fraction}'
+        #end if
     ]]></command>
     <inputs>
-        <param label="First Read Input (FASTQ)" name="input1" type="data" format="fastq" />
-        <param label="Second Read Input (FASTQ)" name="input2" type="data" format="fastq" />
-        <param label="Merge Reads" name="merge_reads" type="boolean" truevalue="true" falsevalue="false" checked="true"/>
+        <param label="First Read Input (FASTQ)" name="input1" type="data" format="fastq" help="Select the FASTQ file containing the first set of paired-end reads."/>
+        <param label="Second Read Input (FASTQ)" name="input2" type="data" format="fastq" help="Select the FASTQ file containing the second set of paired-end reads."/>
+        <param label="Merge Reads" name="merge_reads" type="boolean" truevalue="true" falsevalue="false" checked="true" help="Enable this to merge overlapping reads from the provided paired-end FASTQ files."/>        
 
         <!-- Section for General Arguments -->
         <section name="general_options" title="General Arguments (Optional)" expanded="false">
@@ -111,7 +111,7 @@
             <param label="Minimum Length of Reads" name="min_length" argument="-L" type="integer" optional="true" value="30" help="Minimum length of a trimmed or merged read to print it" />
         </section>
 
-        <!-- Section for Additional Adapter/Primer Trimming Arguments -->
+        <!-- Section fo\r Additional Adapter/Primer Trimming Arguments -->
         <section name="trimming_options" title="Additional Adapter/Primer Trimming Arguments" expanded="false">
             <param name="adapter_a" argument="-A" label="Adapter Sequence A" type="text" optional="true" value="AGATCGGAAGAGCGGTTCAG" help="Forward read primer/adapter sequence to trim as it would appear at the end of a read" />
             <param name="adapter_b" argument="-B" label="Adapter Sequence B" type="text" optional="true" value="AGATCGGAAGAGCGTCGTGT" help="Reverse read primer/adapter sequence to trim as it would appear at the end of a read" />
@@ -299,6 +299,19 @@
             <output name="output1" file="output1_adapter_trim.fq.gz" />
             <output name="output2" file="output2_adapter_trim.fq.gz" />
         </test>
+
+        
+        <!-- Test with gzipped input files #6 -->
+        <test expect_num_outputs="3">
+            <param name="input1" value="input1.fastq.gz" />
+            <param name="input2" value="input2.fastq.gz" />
+            <param name="merge_reads" value="true" />
+
+            <!-- Expected Outputs -->
+            <output name="output1" file="output1_from_gzipped.fq.gz" />
+            <output name="output2" file="output2_from_gzipped.fq.gz" />
+            <output name="merged" file="merged_output_from_gzipped.fq.gz" />
+        </test>
     </tests>
     <help><![CDATA[
     **SeqPrep**
@@ -317,11 +330,19 @@
 
     **Outputs**
 
-    SeqPrep generates outputs in gzipped FASTQ format. Depending on your settings, this may include:
+    SeqPrep generates outputs in gzipped FASTQ format.
+
+    See more details on SeqPrep github repository: https://github.com/jstjohn/SeqPrep
+
+    **License**
+
+    SeqPrep is copyrighted to John St. John.
+
+    This wrapper is copyrighted by Lionel Guy, and is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
 
-    - Individual read files (if they are not fully merged).
-    - A combined read file with merged reads.
+    This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
 
+    You should have received a copy of the GNU General Public License along with this program.  If not, see http://www.gnu.org/licenses/.
     ]]></help>
     <expand macro="citations"/>
 </tool>
\ No newline at end of file
diff --git a/tools/seqprep/test-data/input1.fastq.gz b/tools/seqprep/test-data/input1.fastq.gz
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S%?U$bdin=CM)~0z5&!_pXnAV@

literal 0
HcmV?d00001


From 6537325a4f342be4e7337ae30bdfd837f8d98664 Mon Sep 17 00:00:00 2001
From: Albert <ratschinski.albert@gmail.com>
Date: Mon, 22 Jan 2024 13:20:37 +0100
Subject: [PATCH 7/9] Adjusted spacing in seprep.xml

---
 tools/seqprep/seqprep.xml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/seqprep/seqprep.xml b/tools/seqprep/seqprep.xml
index b7084f4562f..f2d194d0601 100644
--- a/tools/seqprep/seqprep.xml
+++ b/tools/seqprep/seqprep.xml
@@ -98,9 +98,9 @@
         #end if
     ]]></command>
     <inputs>
-        <param label="First Read Input (FASTQ)" name="input1" type="data" format="fastq" help="Select the FASTQ file containing the first set of paired-end reads."/>
-        <param label="Second Read Input (FASTQ)" name="input2" type="data" format="fastq" help="Select the FASTQ file containing the second set of paired-end reads."/>
-        <param label="Merge Reads" name="merge_reads" type="boolean" truevalue="true" falsevalue="false" checked="true" help="Enable this to merge overlapping reads from the provided paired-end FASTQ files."/>        
+        <param label="First Read Input (FASTQ)" name="input1" type="data" format="fastq" help="Select the FASTQ file containing the first set of paired-end reads." />
+        <param label="Second Read Input (FASTQ)" name="input2" type="data" format="fastq" help="Select the FASTQ file containing the second set of paired-end reads." />
+        <param label="Merge Reads" name="merge_reads" type="boolean" truevalue="true" falsevalue="false" checked="true" help="Enable this to merge overlapping reads from the provided paired-end FASTQ files." />        
 
         <!-- Section for General Arguments -->
         <section name="general_options" title="General Arguments (Optional)" expanded="false">
@@ -111,7 +111,7 @@
             <param label="Minimum Length of Reads" name="min_length" argument="-L" type="integer" optional="true" value="30" help="Minimum length of a trimmed or merged read to print it" />
         </section>
 
-        <!-- Section fo\r Additional Adapter/Primer Trimming Arguments -->
+        <!-- Section for Additional Adapter/Primer Trimming Arguments -->
         <section name="trimming_options" title="Additional Adapter/Primer Trimming Arguments" expanded="false">
             <param name="adapter_a" argument="-A" label="Adapter Sequence A" type="text" optional="true" value="AGATCGGAAGAGCGGTTCAG" help="Forward read primer/adapter sequence to trim as it would appear at the end of a read" />
             <param name="adapter_b" argument="-B" label="Adapter Sequence B" type="text" optional="true" value="AGATCGGAAGAGCGTCGTGT" help="Reverse read primer/adapter sequence to trim as it would appear at the end of a read" />

From c95a4b0a6be595e0157cdd3e265b3a1577b18016 Mon Sep 17 00:00:00 2001
From: RZ9082 <randzoabi.rz@gmail.com>
Date: Wed, 31 Jan 2024 16:17:50 +0100
Subject: [PATCH 8/9] added license and creators

---
 tools/seqprep/macros.xml  |  8 ++++++++
 tools/seqprep/seqprep.xml | 13 ++++---------
 2 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/tools/seqprep/macros.xml b/tools/seqprep/macros.xml
index 7cb56039a3e..81ae1901af9 100644
--- a/tools/seqprep/macros.xml
+++ b/tools/seqprep/macros.xml
@@ -11,6 +11,14 @@
             <xref type="bio.tools">seqprep</xref>
         </xrefs>
     </xml>
+    <xml name="creators">
+        <creator>
+            <person givenName="John" familyName="St. John" url="https://github.com/jstjohn" />
+            <person givenName="Lionel" familyName="Guy" />
+            <person givenName="John" familyName="Chilton" url="https://github.com/jmchilton" />
+            <person givenName="Albert" familyName="Ratschinski" url="https://github.com/Alby-Git" />
+        </creator>
+    </xml>
     <xml name="citations">
         <citations>
             <citation type="bibtex">
diff --git a/tools/seqprep/seqprep.xml b/tools/seqprep/seqprep.xml
index f2d194d0601..ab487174249 100644
--- a/tools/seqprep/seqprep.xml
+++ b/tools/seqprep/seqprep.xml
@@ -5,6 +5,7 @@
     </macros>
     <expand macro="biotools"/>
     <expand macro="requirements"/>
+    <expand macro="creators"/>
     <command detect_errors="exit_code"><![CDATA[
         SeqPrep
         -f '${input1}'
@@ -98,8 +99,8 @@
         #end if
     ]]></command>
     <inputs>
-        <param label="First Read Input (FASTQ)" name="input1" type="data" format="fastq" help="Select the FASTQ file containing the first set of paired-end reads." />
-        <param label="Second Read Input (FASTQ)" name="input2" type="data" format="fastq" help="Select the FASTQ file containing the second set of paired-end reads." />
+        <param label="First Read Input" name="input1" type="data" format="fastq" help="Select the FASTQ file containing the first set of paired-end reads." />
+        <param label="Second Read Input" name="input2" type="data" format="fastq" help="Select the FASTQ file containing the second set of paired-end reads." />
         <param label="Merge Reads" name="merge_reads" type="boolean" truevalue="true" falsevalue="false" checked="true" help="Enable this to merge overlapping reads from the provided paired-end FASTQ files." />        
 
         <!-- Section for General Arguments -->
@@ -336,13 +337,7 @@
 
     **License**
 
-    SeqPrep is copyrighted to John St. John.
-
-    This wrapper is copyrighted by Lionel Guy, and is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-
-    This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License along with this program.  If not, see http://www.gnu.org/licenses/.
+    `MIT <https://raw.githubusercontent.com/jstjohn/SeqPrep/master/LICENSE>`_
     ]]></help>
     <expand macro="citations"/>
 </tool>
\ No newline at end of file

From c880b629b88d69141421daa143bfaece78557c97 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Sun, 11 Feb 2024 00:07:49 +0100
Subject: [PATCH 9/9] cosmetic changes

---
 tools/seqprep/seqprep.xml | 42 +++++++++++----------------------------
 1 file changed, 12 insertions(+), 30 deletions(-)

diff --git a/tools/seqprep/seqprep.xml b/tools/seqprep/seqprep.xml
index ab487174249..dd55c8f2e11 100644
--- a/tools/seqprep/seqprep.xml
+++ b/tools/seqprep/seqprep.xml
@@ -7,7 +7,7 @@
     <expand macro="requirements"/>
     <expand macro="creators"/>
     <command detect_errors="exit_code"><![CDATA[
-        SeqPrep
+    SeqPrep
         -f '${input1}'
         -r '${input2}'
         -1 '${output1}'
@@ -99,17 +99,17 @@
         #end if
     ]]></command>
     <inputs>
-        <param label="First Read Input" name="input1" type="data" format="fastq" help="Select the FASTQ file containing the first set of paired-end reads." />
-        <param label="Second Read Input" name="input2" type="data" format="fastq" help="Select the FASTQ file containing the second set of paired-end reads." />
-        <param label="Merge Reads" name="merge_reads" type="boolean" truevalue="true" falsevalue="false" checked="true" help="Enable this to merge overlapping reads from the provided paired-end FASTQ files." />        
+        <param name="input1" type="data" format="fastq" label="First Read Input" help="Select the FASTQ file containing the first set of paired-end reads." />
+        <param name="input2" type="data" format="fastq" label="Second Read Input" help="Select the FASTQ file containing the second set of paired-end reads." />
+        <param name="merge_reads" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Merge Reads" help="Enable this to merge overlapping reads from the provided paired-end FASTQ files." />        
 
         <!-- Section for General Arguments -->
         <section name="general_options" title="General Arguments (Optional)" expanded="false">
-            <param label="First Read Discarded FASTQ Filename" name="first_read_discarded" argument="-3" type="text" optional="true" help="first read discarded fastq filename" />
-            <param label="Second Read Discarded FASTQ Filename" name="second_read_discarded" argument="-4" type="text" optional="true" help="second read discarded fastq filename" />
-            <param label="Input Sequence is in Phred+64 Format" name="phred64" argument="-6" type="boolean" truevalue="-6" falsevalue="" checked="false" help="Input sequence is in phred+64 rather than phred+33 format, the output will still be phred+33"/>
-            <param label="Quality Score Cutoff" name="quality_cutoff" argument="-q" type="integer" optional="true" value="13" help="Quality score cutoff for mismatches to be counted in overlap" />
-            <param label="Minimum Length of Reads" name="min_length" argument="-L" type="integer" optional="true" value="30" help="Minimum length of a trimmed or merged read to print it" />
+            <param name="first_read_discarded" argument="-3" type="text" optional="true" label="First Read Discarded FASTQ Filename" help="first read discarded fastq filename" />
+            <param name="second_read_discarded" argument="-4" type="text" optional="true" label="Second Read Discarded FASTQ Filename" help="second read discarded fastq filename" />
+            <param name="phred64" argument="-6" type="boolean" truevalue="-6" falsevalue="" checked="false" label="Input Sequence is in Phred+64 Format" help="Input sequence is in phred+64 rather than phred+33 format, the output will still be phred+33"/>
+            <param name="quality_cutoff" argument="-q" type="integer" optional="true" value="13" label="Quality Score Cutoff" help="Quality score cutoff for mismatches to be counted in overlap" />
+            <param name="min_length" argument="-L" type="integer" optional="true" value="30" label="Minimum Length of Reads" help="Minimum length of a trimmed or merged read to print it" />
         </section>
 
         <!-- Section for Additional Adapter/Primer Trimming Arguments -->
@@ -182,8 +182,6 @@
                 <param name="read_alignment_gap_end" value="5" />
                 <param name="read_alignment_max_gap_fraction" value="0.125" />
             </section>
-
-            <!-- Outputs -->
             <output name="output1" file="output1.fq.gz" />
             <output name="output2" file="output2.fq.gz" />
             <output name="merged" file="merged_output.fq.gz" />
@@ -219,19 +217,15 @@
                 <param name="read_alignment_gap_end" value="5" />
                 <param name="read_alignment_max_gap_fraction" value="0.125" />
             </section>
-
-            <!-- Outputs -->
             <output name="output1" file="outputNoMerge1.fq.gz" />
             <output name="output2" file="outputNoMerge2.fq.gz" />
         </test>
-
         <!-- Test with Empty Input Files #3 -->
         <test expect_num_outputs="3">
             <param name="input1" value="empty1.fq" />
             <param name="input2" value="empty2.fq" />
             <param name="merge_reads" value="true" />
 
-
             <!-- Section for General Arguments -->
             <section name="general_options" >
                 <param name="quality_cutoff" value="13" />
@@ -256,8 +250,6 @@
                 <param name="read_alignment_gap_end" value="5" />
                 <param name="read_alignment_max_gap_fraction" value="0.125" />
             </section>
-
-            <!-- Outputs -->
             <output name="output1" file="empty_output1.fq.gz" />
             <output name="output2" file="empty_output2.fq.gz" />
             <output name="merged" file="empty_merged_output.fq.gz" />
@@ -272,8 +264,6 @@
 
             <param name="quality_cutoff" value="15" />
             <param name="min_length" value="25" />
-
-            <!-- Outputs -->
             <output name="output1" file="output1_general_args.fq.gz" />
             <output name="output2" file="output2_general_args.fq.gz" />
         </test>
@@ -295,20 +285,14 @@
                 <param name="gap_end" value="3" />
                 <param name="local_alignment_score" value="28" />
             </section>
-
-            <!-- Outputs -->
             <output name="output1" file="output1_adapter_trim.fq.gz" />
             <output name="output2" file="output2_adapter_trim.fq.gz" />
         </test>
-
-        
         <!-- Test with gzipped input files #6 -->
         <test expect_num_outputs="3">
             <param name="input1" value="input1.fastq.gz" />
             <param name="input2" value="input2.fastq.gz" />
             <param name="merge_reads" value="true" />
-
-            <!-- Expected Outputs -->
             <output name="output1" file="output1_from_gzipped.fq.gz" />
             <output name="output2" file="output2_from_gzipped.fq.gz" />
             <output name="merged" file="merged_output_from_gzipped.fq.gz" />
@@ -317,7 +301,8 @@
     <help><![CDATA[
     **SeqPrep**
     
-    SeqPrep is a versatile tool designed for merging overlapping paired-end Illumina reads into a single, longer read. Additionally, it offers the functionality to trim adapter sequences from reads, making it an needful tool for preprocessing Illumina sequencing data.
+    SeqPrep is a versatile tool designed for merging overlapping paired-end Illumina reads into a single, longer read. Additionally, it offers the functionality to trim adapter sequences from reads, making it
+    a needful tool for preprocessing Illumina sequencing data.
 
     **Usage**
 
@@ -335,9 +320,6 @@
 
     See more details on SeqPrep github repository: https://github.com/jstjohn/SeqPrep
 
-    **License**
-
-    `MIT <https://raw.githubusercontent.com/jstjohn/SeqPrep/master/LICENSE>`_
     ]]></help>
     <expand macro="citations"/>
-</tool>
\ No newline at end of file
+</tool>