view coverage.xml @ 5:9410f163f2e7 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb

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