Updating tools/bowtie2 from version 2.5.0 to 2.5.3 (galaxyproject#5118)

* Updating tools/bowtie2 from version 2.5.0 to 2.5.1 * Updating tools/bowtie2 from version 2.5.1 to 2.5.2 * Updating tools/bowtie2 from version 2.5.2 to 2.5.3 * update test data * fix some lints * fix a few more lint errors --------- Co-authored-by: planemo-autoupdate <[email protected]> Co-authored-by: planemo-autoupdate <[email protected]> Co-authored-by: Bjoern Gruening <[email protected]> Co-authored-by: Björn Grüning <[email protected]>
pavanvidem · Feb 26, 2024 · f25b49b · f25b49b
1 parent eb09ed8
commit f25b49b
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Showing 7 changed files with 17 additions and 18 deletions.
diff --git a/tools/bowtie2/bowtie2_macros.xml b/tools/bowtie2/bowtie2_macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.5.0</token>
+    <token name="@TOOL_VERSION@">2.5.3</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <!-- Import this at the top of your command block and then
          define rg_auto_name. -->
@@ -310,11 +310,11 @@
                     <option value="--rf">--rf</option>
                     <option value="--ff">--ff</option>
                 </param>
-                <param argument="--no-mixed" name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/>
-                <param argument="--no-discordant" name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/>
-                <param argument="--dovetail" name="dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/>
-                <param argument="--no-contain" name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Disallow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/>
-                <param argument="--no-overlap" name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Disallow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/>
+                <param argument="--no-mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/>
+                <param argument="--no-discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/>
+                <param argument="--dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/>
+                <param argument="--no-contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Disallow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/>
+                <param argument="--no-overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Disallow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/>
             </when>
             <when value="no">
                 <!-- do nothing -->

diff --git a/tools/bowtie2/bowtie2_wrapper.xml b/tools/bowtie2/bowtie2_wrapper.xml
@@ -1,4 +1,4 @@
-<tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
+<tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <description>- map reads against reference genome</description>
     <macros>
         <import>bowtie2_macros.xml</import>
@@ -8,7 +8,7 @@
     </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement>
-        <requirement type="package" version="1.16.1">samtools</requirement>
+        <requirement type="package" version="1.19.2">samtools</requirement>
     </requirements>
     <version_command>bowtie2 --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
@@ -68,7 +68,7 @@ set -o | grep -q pipefail && set -o pipefail;
     #else:
         #set read1 = "input_f.fastq"
     #end if
-    ln -s '${library.input_1.forward}' ${read1} &&
+    ln -f -s '${library.input_1.forward}' ${read1} &&
 
     #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
         #set read2 = "input_r.fastq.gz"
@@ -81,7 +81,7 @@ set -o | grep -q pipefail && set -o pipefail;
     #else:
         #set read2 = "input_r.fastq"
     #end if
-    ln -s '${library.input_1.reverse}' ${read2} &&
+    ln -f -s '${library.input_1.reverse}' ${read2} &&
 
 #else if str($library.type) == 'paired_interleaved':
     #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
@@ -96,7 +96,7 @@ set -o | grep -q pipefail && set -o pipefail;
     #else:
         #set read1 = "input_il.fastq"
     #end if
-    ln -s '${library.input_1}' ${read1} &&
+    ln -f -s '${library.input_1}' ${read1} &&
 #else:
     #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
         #set read1 = "input_f.fastq.gz"
@@ -110,7 +110,7 @@ set -o | grep -q pipefail && set -o pipefail;
     #else:
         #set read1 = "input_f.fastq"
     #end if
-    ln -s '${library.input_1}' ${read1} &&
+    ln -f -s '${library.input_1}' ${read1} &&
 #end if
 
 ## execute bowtie2
@@ -339,7 +339,6 @@ bowtie2
               <option value="paired_collection">Paired-end Dataset Collection</option>
               <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
             </param>
-
             <when value="single">
                 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
                 <expand macro="align_unalign" />
@@ -523,12 +522,12 @@ bowtie2
             </param>
             <when value="yes">
                 <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/>
-                <param name="no_unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/>
-                <param name="omit_sec_seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/>
-                <param name="sam_no_qname_trunc" argument="--sam-no-qname-trunc" type="boolean" truevalue="--sam-no-qname-trunc" falsevalue="" label="Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM"/>
+                <param argument="--no-unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/>
+                <param argument="--omit-sec-seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/>
+                <param argument="--sam-no-qname-trunc" type="boolean" truevalue="--sam-no-qname-trunc" falsevalue="" label="Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM"/>
                 <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/>
-                <param name="soft_clipped_unmapped_tlen" argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/>
-                <param name="reorder" argument="--reorder" type="boolean" truevalue="--reorder" falsevalue=""
+                <param argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/>
+                <param argument="--reorder" type="boolean" truevalue="--reorder" falsevalue=""
                     label="Reorder output to reflect order of the input file"
                     help="Reorder guarantees that output SAM records are printed in an order corresponding to the order of the reads in the original input file, even when -p is set greater than 1." />
             </when>

diff --git a/tools/bowtie2/test-data/bowtie2-test1.bam b/tools/bowtie2/test-data/bowtie2-test1.bam
diff --git a/tools/bowtie2/test-data/bowtie2-test2.bam b/tools/bowtie2/test-data/bowtie2-test2.bam
diff --git a/tools/bowtie2/test-data/bowtie2-test_fasta_in.bam b/tools/bowtie2/test-data/bowtie2-test_fasta_in.bam
diff --git a/tools/bowtie2/test-data/bowtie2-test_fasta_in_bam_qname_input_sorted.bam b/tools/bowtie2/test-data/bowtie2-test_fasta_in_bam_qname_input_sorted.bam
diff --git a/tools/bowtie2/test-data/bowtie2-test_il.bam b/tools/bowtie2/test-data/bowtie2-test_il.bam