annotate coverage.xml @ 0:283ab3112eea draft

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

<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>