diff coverage.xml @ 0:283ab3112eea draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 29b0ab3564dcf719bdb8ebd19d8b0956b0990e7a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/coverage.xml	Tue May 16 13:14:57 2023 +0000
@@ -0,0 +1,70 @@
+<tool id="cnvkit_coverage" name="CNVkit Coverage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Calculate coverage in the given regions from BAM read depths</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[  
+        ln -s '$input_bam_file' ./tumor.bam &&
+        ln -s '$input_interval_bed' ./capture.split.bed &&
+        #if $reference_source.fasta
+            #if str($reference_source.ref_selector) == 'history':
+                ln -s '$reference_source.fasta' ./genome.fa &&
+                samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for CNVkit' >&2 &&
+            #else
+                ln -s '$reference_source.fasta.fields.path' ./genome.fa &&
+                ln -s '${reference_source.fasta.fields.path}.fai' ./genome.fa.fai &&
+            #end if
+        #end if
+        #import os
+        cnvkit.py coverage
+            ./tumor.bam
+            ./capture.split.bed
+            --output sample.targetcoverage.cnn
+            --processes \${GALAXY_SLOTS:-4}
+            $count
+            #if str($min_mapq)
+                --min-mapq $min_mapq
+            #end if
+    ]]></command>
+    <inputs>
+        <param name="input_bam_file" type="data" format="bam" label="Sample BAM file" help="" />
+        <param name="input_interval_bed" type="data" format="bed" label="Interval BED file" help="" />
+        <expand macro="reference_interface"/>
+        <param argument="--count" type="boolean" checked="false" truevalue="--count" falsevalue="" label="Get read depths by counting read midpoints within each bin" help="" />
+        <param argument="--min-mapq" optional="true" type="integer" label="Minimum mapping quality score to count a read for coverage depth" min="0" max="60" value="0" help="" />
+    </inputs>
+    <outputs>
+        <data name="out_capture_target_coverage" format="tabular" label="${tool.name} on ${on_string}: Sample Target coverage" from_work_dir="sample.targetcoverage.cnn" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <conditional name="reference_source">
+                <param name="ref_selector" value="history"/>
+                <param name="fasta" ftype="fasta" value="genome.fasta" />
+            </conditional>
+            <param name="input_bam_file" ftype="bam" value="tumor.bam" />
+            <param name="input_interval_bed" ftype="bed" value="capture.split.bed" />
+            <output name="out_capture_target_coverage" file="sample.targetcoverage.cnn" /> 
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="reference_source">
+                <param name="ref_selector" value="cached"/>
+                <param name="fasta" value="test_buildid"/>
+            </conditional>
+            <param name="input_bam_file" ftype="bam" value="tumor.bam" />
+            <param name="input_interval_bed" ftype="bed" value="capture.split.bed" />
+            <output name="out_capture_target_coverage" file="sample.targetcoverage.cnn" /> 
+        </test>
+    </tests>
+    <help><![CDATA[
+         Summary statistics of read counts and their binning are printed to standard error
+         when CNVkit finishes calculating the coverage of each sample (through either the
+         batch or coverage commands)
+         
+         Target and antitarget bin-level coverages (.cnn) output file contains those columns
+          chromosome, Start, end, gene, log2 and depth
+    ]]></help>
+    <expand macro="citations" />
+</tool>