view vcf.xml @ 0:4cf5a2dd27dd draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71

<tool id="cnvkit_export_vcf" name="CNVkit Export VCF" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>Converts the Segmented copy ratio data file (*.cns) file into VCF file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="creators"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[  
        ln -s '$input_segmented_file' ./sample.cns &&
        ln -s '$advanced_settings.cnr' ./sample.cnr &&
        cnvkit.py export vcf
            ./sample.cns
            #if $advanced_settings.cnr
              --cnr ./sample.cnr
            #end if
            #if $advanced_settings.sample_id
              --sample-id '$advanced_settings.sample_id'
            #end if
            #if $advanced_settings.ploidy
              --ploidy $advanced_settings.ploidy
            #end if
            #if str($advanced_settings.sample_sex) and $advanced_settings.sample_sex != ""
              --sample-sex '$advanced_settings.sample_sex'
            #end if
            $advanced_settings.male_reference  
            --output sample.cnv.vcf
            #if $advanced_settings.diploid_parx_genome
              --diploid-parx-genome '$advanced_settings.diploid_parx_genome'
            #end if
    ]]></command>
     <inputs>
        <param name="input_segmented_file" type="data" format="tabular" label="Segmented Copy Ratio Data File (cns file)" help="" />
        <section name="advanced_settings" title="Advanced settings" expanded="false">
            <param argument="--cnr" optional="true" type="data" format="tabular" label="Bin-level copy ratios (cnr)" help="" />
            <param argument="--sample-id" optional="true" type="text" label="Sample ID" value="" help="Sample name to write in the genotype field of the output VCF file" />
            <param argument="--ploidy" optional="true" type="integer" label="Ploidy" min="1" value="2" help="Ploidy of the sample cells. [Default: 2]" />
            <expand macro="sample_sex"/>
            <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="MALE REFERENCE" help="Assume inputs were normalized to a male reference" />
            <param argument="--diploid-parx-genome" optional="true" type="text" label="Diploid Parx Genome" value="" help="Considers the given human genome's PAR of chromosome X as autosomal. Example: 'grch38'" />
        </section>  
        </inputs>
    <outputs>
        <data name="CNVs_VCF" format="vcf" label="${tool.name} on ${on_string}: CNVs VCF file" from_work_dir="sample.cnv.vcf" />
    </outputs>
       <tests>
        <test expect_num_outputs="1">
            <param name="input_segmented_file" ftype="tabular" value="sample.cns" />
            <param name="sample_id" value="SampleID" />
            <param name="sample_sex" value="Female" />
            <output name="CNVs_VCF" file="sample.cnv.vcf" ftype="vcf" lines_diff="2" />
        </test>
    </tests>
    <help><![CDATA[
        Export the segmented copy number data (from a .cns file) to the standard VCF 4.2 format. 
        The resulting VCF file describes copy number gains and losses across each segment and contains 
        INFO fields for breakpoints (CIPOS, CIEND) if bin-level data (.cnr) is provided.
    ]]></help>
    <expand macro="citations" />
</tool>