comparison strelka.xml @ 3:4e6e20c9738b draft default tip

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2:3ce78c04c7e5

    </description>
    <macros>
        <import>citations.xml</import>
    </macros>    
    <requirements>
	<requirement type="package" version="1.0.14">strelka</requirement>
    </requirements>
    <command detect_errors="aggressive">

    ln -s $normal normal.bam;
    ln -s $normal.metadata.bam_index normal.bam.bai;

        
        done;
        
    #else

        cat ./strelkaAnalysis/results/all.somatic.snvs.vcf > $snvs;
        cat ./strelkaAnalysis/results/all.somatic.indels.vcf > $indels; 

    #end if

    </command>
    <inputs>
	<conditional name="reference_source">
            <param label="Choose the source for the reference genome" name="reference_source_selector" type="select">
                <option value="cached">Use a built-in genome</option>
                <option value="history">Use a genome from the history</option>
            </param>
            <when value="cached">

    </outputs>
    <tests>
        <test>
            <param name="normal" value="test.normal.bam"/>
            <param name="normal.metadata.bam_index" value="test.normal.bam.bai"/>
	          <param name="tumour" value="test.tumour.bam"/>
	          <param name="tumour.metadata.bam_index" value="test.tumour.bam.bai"/>
            <param name="reference_source.reference_source_selector" value="history"/>
            <param name="reference_source.ref_file" value="test.fa"/>
            <output name="snvs" ftype="vcf" file="all.somatic.snvs.vcf" lines_diff="2"/>
        </test>
    </tests>

3:4e6e20c9738b

    </description>
    <macros>
        <import>citations.xml</import>
    </macros>    
    <requirements>
<requirement type="package" version="1.0.14">strelka</requirement>
    </requirements>
    <command detect_errors="aggressive">

    ln -s $normal normal.bam;
    ln -s $normal.metadata.bam_index normal.bam.bai;

        
        done;
        
    #else

        cat ./strelkaAnalysis/results/passed.somatic.snvs.vcf > $snvs;
        cat ./strelkaAnalysis/results/padded.somatic.indels.vcf > $indels; 

    #end if

    </command>
    <inputs>
<conditional name="reference_source">
            <param label="Choose the source for the reference genome" name="reference_source_selector" type="select">
                <option value="cached">Use a built-in genome</option>
                <option value="history">Use a genome from the history</option>
            </param>
            <when value="cached">

    </outputs>
    <tests>
        <test>
            <param name="normal" value="test.normal.bam"/>
            <param name="normal.metadata.bam_index" value="test.normal.bam.bai"/>
          <param name="tumour" value="test.tumour.bam"/>
          <param name="tumour.metadata.bam_index" value="test.tumour.bam.bai"/>
            <param name="reference_source.reference_source_selector" value="history"/>
            <param name="reference_source.ref_file" value="test.fa"/>
            <output name="snvs" ftype="vcf" file="all.somatic.snvs.vcf" lines_diff="2"/>
        </test>
    </tests>