Merge pull request #16668 from bernt-matthias/topic/samtools-bump

Bump samtools converters
galaxyproject · Sep 10, 2023 · f43f350 · f43f350
2 parents 174257d + b2a3208
commit f43f350
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Showing 10 changed files with 42 additions and 26 deletions.
diff --git a/lib/galaxy/datatypes/converters/bam_to_bai.xml b/lib/galaxy/datatypes/converters/bam_to_bai.xml
@@ -1,8 +1,8 @@
-<tool id="CONVERTER_Bam_Bai_0" name="Convert Bam to Bai" version="1.0.0" hidden="true" profile="16.04">
+<tool id="CONVERTER_Bam_Bai_0" name="Convert Bam to Bai" version="1.0.1" hidden="true" profile="16.04">
     <requirements>
-        <requirement type="package" version="1.10">samtools</requirement>
+        <requirement type="package" version="1.17">samtools</requirement>
     </requirements>
-    <command>samtools index -@ \${GALAXY_SLOTS:-1} '$input1' '$output1'</command>
+    <command>samtools index -@ \${GALAXY_SLOTS:-1} -b '$input1' -o '$output1'</command>
     <inputs>
         <param format="bam" name="input1" type="data" label="Choose BAM"/>
     </inputs>
@@ -12,7 +12,11 @@
     <tests>
         <test>
             <param name="input1" ftype="bam" value="srma_out2.bam"/>
-            <output name="output1" ftype="bai" value="srma_out2.bai"/>
+            <output name="output1" ftype="bai">
+                <assert_contents>
+                    <has_size value="7584" delta="10"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help>

diff --git a/lib/galaxy/datatypes/converters/cram_to_bam_converter.xml b/lib/galaxy/datatypes/converters/cram_to_bam_converter.xml
@@ -1,6 +1,6 @@
-<tool id="CONVERTER_cram_to_bam_0" name="Convert CRAM to BAM" version="1.0.1" hidden="true" profile="16.04">
+<tool id="CONVERTER_cram_to_bam_0" name="Convert CRAM to BAM" version="1.0.2" hidden="true" profile="16.04">
     <requirements>
-        <requirement type="package" version="1.16.1">samtools</requirement>
+        <requirement type="package" version="1.17">samtools</requirement>
     </requirements>
     <command><![CDATA[
         samtools sort -@\${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$output' --output-fmt BAM '$input'

diff --git a/lib/galaxy/datatypes/converters/fasta_to_fai.xml b/lib/galaxy/datatypes/converters/fasta_to_fai.xml
@@ -1,6 +1,6 @@
-<tool id="CONVERTER_fasta_to_fai" name="Convert FASTA to fai file" version="1.0.0">
+<tool id="CONVERTER_fasta_to_fai" name="Convert FASTA to fai file" version="1.0.1">
     <requirements>
-        <requirement type="package" version="0.1.19">samtools</requirement>
+        <requirement type="package" version="1.17">samtools</requirement>
     </requirements>
     <command><![CDATA[
 ln -s '$input' temp.fasta &&

diff --git a/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
@@ -1,8 +1,8 @@
-<tool id="CONVERTER_sam_to_bigwig_0" name="Convert SAM to BigWig" version="1.0.2" hidden="true">
+<tool id="CONVERTER_sam_to_bigwig_0" name="Convert SAM to BigWig" version="1.0.3" hidden="true">
     <requirements>
-        <requirement type="package" version="357">ucsc-bedgraphtobigwig</requirement>
-        <requirement type="package" version="1.6">samtools</requirement>
-        <requirement type="package" version="2.27.1">bedtools</requirement>
+        <requirement type="package" version="445">ucsc-bedgraphtobigwig</requirement>
+        <requirement type="package" version="1.17">samtools</requirement>
+        <requirement type="package" version="2.31.0">bedtools</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
 samtools view -bh '$input' | bedtools genomecov -bg -split -ibam stdin

diff --git a/lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml b/lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml
@@ -1,12 +1,13 @@
-<tool id="CONVERTER_sam_to_unsorted_bam" name="Convert SAM to BAM without sorting" version="1.0.0" profile="18.01">
+<tool id="CONVERTER_sam_to_unsorted_bam" name="Convert SAM to BAM without sorting" version="1.0.1" profile="18.01">
     <requirements>
-        <requirement type="package" version="1.6">samtools</requirement>
+        <requirement type="package" version="1.17">samtools</requirement>
     </requirements>
     <command><![CDATA[
         samtools view
             -b
             -h
             -@ \${GALAXY_SLOTS:-2}
+            --no-PG
             -o '${output}'
             '$input'
     ]]>

diff --git a/lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml b/lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
@@ -1,13 +1,14 @@
-<tool id="CONVERTER_bam_to_coodinate_sorted_bam" name="Convert BAM to coordinate-sorted BAM" version="1.0.0" hidden="true" profile="18.01">
+<tool id="CONVERTER_bam_to_coodinate_sorted_bam" name="Convert BAM to coordinate-sorted BAM" version="1.0.1" hidden="true" profile="18.01">
     <requirements>
-        <requirement type="package" version="1.6">samtools</requirement>
+        <requirement type="package" version="1.17">samtools</requirement>
     </requirements>
     <command><![CDATA[
          samtools sort
             -@ \${GALAXY_SLOTS:-1}
+            --no-PG
             -o '${output}'
             -O bam
-            -T dataset
+            -T "\${TMPDIR:-.}"
             '${input}'
     ]]>
     </command>
@@ -20,7 +21,8 @@
     <tests>
         <test>
             <param name="input" ftype="sam" value="bfast_out1.sam"/>
-            <output name="output" ftype="bam" value="bfast_out1.bam"/>
+            <!--lines diff due to @HD line which contained GO:none before-->
+            <output name="output" ftype="bam" value="bfast_out1.bam" lines_diff="2"/>
         </test>
     </tests>
     <help>

diff --git a/lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml b/lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
@@ -1,14 +1,15 @@
-<tool id="CONVERTER_bam_to_qname_sorted_bam" name="Convert BAM to queryname-sorted BAM" version="1.0.0" hidden="true" profile="18.01">
+<tool id="CONVERTER_bam_to_qname_sorted_bam" name="Convert BAM to queryname-sorted BAM" version="1.0.1" hidden="true" profile="18.01">
     <requirements>
-        <requirement type="package" version="1.6">samtools</requirement>
+        <requirement type="package" version="1.17">samtools</requirement>
     </requirements>
     <command><![CDATA[
          samtools sort
             -@ \${GALAXY_SLOTS:-1}
             -o '${output}'
             -n
+            --no-PG
             -O bam
-            -T dataset
+            -T "\${TMPDIR:-.}" 
             '${input}'
     ]]>
     </command>
@@ -21,7 +22,8 @@
     <tests>
         <test>
             <param name="input" ftype="sam" value="bfast_out1.sam"/>
-            <output name="output" ftype="qname_sorted.bam" value="bfast_out1.qname_sorted.bam"/>
+            <!--lines diff due to @HD line which contained GO:none before-->
+            <output name="output" ftype="qname_sorted.bam" value="bfast_out1.qname_sorted.bam" lines_diff="2"/>
         </test>
     </tests>
     <help>

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
@@ -298,6 +298,12 @@ class safe_update(NamedTuple):
     "Show tail1": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
     "sort1": safe_update(parse_version("1.1.0"), parse_version("1.2.0")),
     "CONVERTER_interval_to_bgzip_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
+    "CONVERTER_Bam_Bai_0": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
+    "CONVERTER_cram_to_bam_0": safe_update(parse_version("1.0.1"), parse_version("1.0.2")),
+    "CONVERTER_fasta_to_fai": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
+    "CONVERTER_sam_to_bigwig_0": safe_update(parse_version("1.0.2"), parse_version("1.0.3")),
+    "CONVERTER_bam_to_coodinate_sorted_bam": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
+    "CONVERTER_bam_to_qname_sorted_bam": safe_update(parse_version("1.0.0"), parse_version("1.0.1")),
 }
 
 

diff --git a/test/functional/tools/sam_to_bam.xml b/test/functional/tools/sam_to_bam.xml
@@ -11,7 +11,8 @@ cat '$input1' > '$out_file1'
     <tests>
         <test>
             <param name="input1" value="sam_with_header.sam" ftype="sam"/>
-            <output name="out_file1" file="bam_from_sam.bam" ftype="bam"/>
+            <!-- allow up to 2 differences (4 lines) due to version change of the implicitly running converter  -->
+            <output name="out_file1" file="bam_from_sam.bam" ftype="bam" lines_diff="4"/>
         </test>
     </tests>
     <help>

diff --git a/test/functional/tools/sam_to_unsorted_bam.xml b/test/functional/tools/sam_to_unsorted_bam.xml
@@ -56,17 +56,17 @@
         <!-- Test that sam input is properly converted to bam -->
         <test>
             <param name="input3" value="sam_with_header.sam" ftype="sam"/>
-            <output name="bam_output" file="bam_from_sam.bam" ftype="bam"/>
+            <output name="bam_output" file="bam_from_sam.bam" ftype="bam" lines_diff="2"/>
         </test>
         <!-- Test that sam input is properly converted to qname_sorted.bam -->
         <test>
             <param name="input4" value="sam_with_header.sam" ftype="sam"/>
-            <output name="qname_sorted_bam_output" file="qname_sorted.bam" ftype="qname_sorted.bam"/>
+            <output name="qname_sorted_bam_output" file="qname_sorted.bam" ftype="qname_sorted.bam" lines_diff="2"/>
         </test>
         <!-- Test that sam input is properly converted to qname_sorted.bam (which is qname_input_sorted.bam compatible) -->
         <test>
             <param name="input4" value="sam_with_header.sam" ftype="sam"/>
-            <output name="qname_sorted_bam_output" file="qname_sorted.bam" ftype="qname_sorted.bam"/>
+            <output name="qname_sorted_bam_output" file="qname_sorted.bam" ftype="qname_sorted.bam" lines_diff="2"/>
         </test>
     </tests>
     <help>