[WIP] fixing planemo tests

deeptools · Jan 24, 2025 · 5b63e42 · 5b63e42
1 parent b7ef67e
commit 5b63e42
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Showing 7 changed files with 41 additions and 38 deletions.
diff --git a/galaxy/wrapper/alignmentSieve.xml b/galaxy/wrapper/alignmentSieve.xml
@@ -7,8 +7,6 @@
     <expand macro="requirements"/>
     <command>
 <![CDATA[
-        #import re
-        #set label = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
         ln -s '$bamfile' one.bam &&
         #if $bamfile.ext == 'bam':
             ln -s '${bamfile.metadata.bam_index}' one.bam.bai &&
@@ -18,13 +16,10 @@
         @BINARY@
         @THREADS@
         -b one.bam
-        --label '$label'
         #if $filterRNAstrand:
             --filterRNAstrand '$filterRNAstrand'
         #end if
 
-        $ignoreDuplicates
-
         #if $minMappingQuality:
             --minMappingQuality $minMappingQuality
         #end if
@@ -104,8 +99,6 @@
             <option value="forward">forward</option>
             <option value="reverse">reverse</option>
         </param>
-
-        <expand macro="ignoreDuplicates"/>
         <expand macro="minMappingQuality"/>
         <expand macro="samFlags"/>
         <expand macro="fragLength"/>

diff --git a/galaxy/wrapper/bamCompare.xml b/galaxy/wrapper/bamCompare.xml
@@ -45,7 +45,7 @@
                 #end if
             #end if
 
-            --operation $comparison.type
+            --operation '$comparison.type'
             $exactScaling
 
             #if $comparison.type in ['ratio','log2']:
@@ -187,25 +187,30 @@
             <param name="outFileFormat" value="bedgraph"/>
             <param name="binSize" value="5"/>
             <param name="type" value="ratio"/>
-            <output name="outFileName" file="bamCompare_result1.bg" ftype="bedgraph"/>
+            <output name="outFileName" ftype="bedgraph">
+                <assert_contents>
+                    <has_text_matching expression="chrM\t0\t16569\t1"/>
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="1">
             <param name="bamFile1" value="bowtie2 test1.bam" ftype="bam"/>
             <param name="bamFile2" value="bowtie2 test1.bam" ftype="bam"/>
-            <param name="showAdvancedOpt" value="yes"/>
             <param name="outFileFormat" value="bigwig"/>
             <param name="binSize" value="10"/>
-            <param name="type" value="ratio"/>
+            <conditional name="comparison">
+                <param name="type" value="ratio"/>
+            </conditional>
             <output name="outFileName" file="bamCompare_result2.bw" ftype="bigwig"/>
         </test>
         <!-- Test with BAM and CRAM file as input-->
         <test expect_num_outputs="1">
             <param name="bamFile1" value="testA.bam" ftype="bam"/>
             <param name="bamFile2" value="testA.cram" ftype="cram"/>
-            <param name="showAdvancedOpt" value="yes"/>
             <param name="outFileFormat" value="bedgraph"/>
-            <param name="binSize" value="10"/>
-            <param name="type" value="ratio"/>
+            <conditional name="comparison">
+                <param name="type" value="ratio"/>
+            </conditional>
             <output name="outFileName" ftype="bedgraph">
                 <assert_contents>
                     <has_text_matching expression="3R\t0\t200\t1"/>
@@ -217,10 +222,15 @@
         <test expect_num_outputs="1">
             <param name="bamFile1" value="testA.bam" ftype="bam"/>
             <param name="bamFile2" value="testA.cram" ftype="cram"/>
-            <param name="showAdvancedOpt" value="yes"/>
             <param name="outFileFormat" value="bedgraph"/>
-            <param name="binSize" value="10"/>
-            <param name="type" value="substract"/>
+            <conditional name="scaling">
+                <param name="method" value="own"/>
+                <param name="scaleFactor1" value="1"/>
+                <param name="scaleFactor2" value="1"/>
+            </conditional>
+            <conditional name="comparison">
+                <param name="type" value="subtract"/>
+            </conditional>
             <output name="outFileName" ftype="bedgraph">
                 <assert_contents>
                     <has_text_matching expression="3R\t0\t200\t0"/>
@@ -232,10 +242,11 @@
         <test expect_num_outputs="1">
             <param name="bamFile1" value="testA.bam" ftype="bam"/>
             <param name="bamFile2" value="testB.bam" ftype="bam"/>
-            <param name="showAdvancedOpt" value="yes"/>
             <param name="outFileFormat" value="bedgraph"/>
             <param name="binSize" value="10"/>
-            <param name="type" value="ratio"/>
+            <conditional name="comparison">
+                <param name="type" value="subtract"/>
+            </conditional>
             <param name="pseudocount" value="1 1"/>
             <output name="outFileName" ftype="bedgraph">
                 <assert_contents>
@@ -250,10 +261,13 @@
         <test expect_num_outputs="1">
             <param name="bamFile1" value="testA.bam" ftype="bam"/>
             <param name="bamFile2" value="testB.bam" ftype="bam"/>
-            <param name="showAdvancedOpt" value="yes"/>
+            <conditional name="scaling">
+                <param name="method" value="own"/>
+                <param name="scaleFactor1" value="1"/>
+                <param name="scaleFactor2" value="1"/>
+            </conditional>
             <param name="outFileFormat" value="bedgraph"/>
-            <param name="binSize" value="10"/>
-            <param name="type" value="ratio"/>
+            <param name="showAdvancedOpt" value="yes"/>
             <param name="skipZeroOverZero" value="--skipZeroOverZero"/>
             <output name="outFileName" ftype="bedgraph">
                 <assert_contents>
@@ -267,10 +281,12 @@
         <test expect_num_outputs="1">
             <param name="bamFile1" value="testA.bam" ftype="bam"/>
             <param name="bamFile2" value="testB.bam" ftype="bam"/>
-            <param name="showAdvancedOpt" value="yes"/>
+            <param name="method" value="own"/>
+            <param name="scaleFactor1" value="1"/>
+            <param name="scaleFactor2" value="1"/>
+            <param name="type" value="subtract"/>
             <param name="outFileFormat" value="bedgraph"/>
-            <param name="binSize" value="10"/>
-            <param name="type" value="ratio"/>
+            <param name="showAdvancedOpt" value="yes"/>
             <param name="skipNAs" value="true"/>
             <output name="outFileName" ftype="bedgraph">
                 <assert_contents>

diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml
@@ -5,8 +5,9 @@
     <token name="@GALAXY_VERSION@">23.2</token>
     <xml name="requirements">
         <requirements>
-            <!-- <requirement type="package" version="@TOOL_VERSION@">deeptools</requirement> -->
-            <requirement type="package" version="1.21">samtools</requirement>
+            <container type="docker">quay.io/biocontainers/deeptools:4.0.0--h004ce86_0</container>
+            <!--requirement type="package" version="@TOOL_VERSION@">deeptools</requirement>
+            <requirement type="package" version="1.21">samtools</requirement-->
         </requirements>
         <expand macro="stdio"/>
         <version_command>@BINARY@ --version</version_command>
@@ -552,21 +553,15 @@ is vital to you, select Yes below.">
     </token>
 
     <xml name="blacklist">
-        <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
+        <param argument="--blackListFileName" type="data" format="bed,gtf" optional="true" min="0"
             label="Blacklisted regions in BED/GTF format"
             help="One or more files containing regions to exclude from the analysis"/>
     </xml>
 
     <token name="@blacklist@">
 <![CDATA[
-        #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
-            #set blfiles=[]
-            #for $f in $advancedOpt.blackListFileName:
-                #silent $blfiles.append("'%s'" % $f)
-            #end for
-            #if $blfiles != ["'None'"]:
-                --blackListFileName #echo ' '.join($blfiles)#
-            #end if
+        #if $advancedOpt.blackListFileName:
+            --blackListFileName '$advancedOpt.blackListFileName'
         #end if
 ]]>
     </token>

diff --git a/galaxy/wrapper/plotPCA.xml b/galaxy/wrapper/plotPCA.xml
@@ -77,7 +77,7 @@
             <param name="plotTitle" value="Test Plot" />
             <param name="outFileFormat" value="png" />
             <param name="outFileNameData" value="True" />
-            <output name="outFileName" file="plotPCA_result2.png" ftype="png" compare="sim_size" delta="12000" />
+            <output name="outFileName" file="plotPCA_result1.png" ftype="png" compare="sim_size" delta="12000" />
             <output name="output_outFileNameData" file="plotPCA_result2.tabular" ftype="tabular" lines_diff="2" />
         </test>
     </tests>

diff --git a/galaxy/wrapper/test-data/bamCompare_result1.bg b/galaxy/wrapper/test-data/bamCompare_result1.bg
diff --git a/galaxy/wrapper/test-data/bamCompare_result2.bw b/galaxy/wrapper/test-data/bamCompare_result2.bw
diff --git a/galaxy/wrapper/test-data/plotPCA_result2.png b/galaxy/wrapper/test-data/plotPCA_result2.png