vcfToMageTab.xml

<tool id="mageTab" name="mageTab" version="0.0.1">
    <description></description>
    <requirements>
        <container type="docker">tcgavcf-tool:0.1</container>
    </requirements>
    <command interpreter="python">
vcfToMageTab.py
#if $params.source == "file":
${params.input_yaml}
#else
${idf_yaml}
#end if
${in_vcf} magetab
    </command>
    <inputs>
        <param name='in_vcf' type="data" format="vcf" help="Input VCF" label="InVCF"/>

        <conditional name="params">
          <param type="select" name="source">
            <option value="file">Param File</option>
            <option value="manual">Manual</option>
          </param>
          <when value="manual">
            <param name='expDesign' type='text' value="individual_genetic_characteristics_design" help="the experimental design tag"/>
            <param name='expDesignOntology' type='text' value="MGED Ontology" help="the experimental design term source reference (e.g. MGED, HUGO, etc."/>
            <param name='expDesignFactorName' type='text' value="somatic_variant" help="the experimental design factor name"/>
            <param name='expDesignFactorType' type='text' value="disease_state" help="the experimental design factor type"/>
            <param name='investigationTitle' type='text' value="MC3 Exome Variant Calling project" help="Investigation Title"/>
            <param name='personLastName' type='text' value="Radenbaugh" help="the submitter's last name"/>
            <param name='personFirstName' type='text' value="Amie" help="the submitter's first name"/>
            <param name='personMidInitial' type='text' value="J" help="the submitter's middle initial"/>
            <param name='personEmail' type='text' value="aradenba@soe.ucsc.edu" help="the submitter's email"/>
            <param name='personAddress' type='text' value="University of California Santa Cruz, 1156 High St, Mail Stop CBSE, Santa Cruz, CA 95064, USA" help="the submitter's institutional address"/>
            <param name='personAffiliation' type='text' value="University of California Santa Cruz Genome Institute" help="the submitter's affiliation"/>
            <param name='personRole' type='text' value="submitter" help="the submitter's role"/>
            <param name='pubMedId' type='text' value="25405470" help="the PubMed ID"/>
            <param name='pubAuthors' type='text' value="Radenbaugh AJ, Ma S, Ewing A, Stuart JM, Collisson EA, Zhu J, Haussler D" help="the publication author list"/>
            <param name='pubTitle' type='text' value="RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection" help="the publication title"/>
            <param name='pubStatus' type='text' value="published" help="the publication status"/>
            <param name='expDescription' type='text' value="Detection of somatic variants from the TCGA Whole-Exome Sequencing (WES) and RNA-Seq data using RADIA" help="the description of the experiment"/>
            <param name='protocolNames' type='text' value="ucsc.edu:variant_calling:Illumina_DNASeq:01,ucsc.edu:vcf2maf:Illumina_DNASeq:01" help="the protocol names"/>
            <param name='protocolTypes' type='text' value="Variant Calling,MAF Generation" help="the protocol types"/>
            <param name='protocolDescriptions' type='text' value="Somatic Variant Calling Pipeline: RADIA v1.1.1 (https://github.com/aradenbaugh/radia/),Annotation: SnpEff v3.3_GRCh37.69 (http://snpeff.sourceforge.net/)" help="the protocol descriptions"/>
            <param name='protocolOntologies' type='text' value="MGED Ontology,MGED Ontology" help="the protocol ontologies"/>
            <param name='protocolParameters' type='text' value="" help="the protocol parameters"/>
            <param name='ontologyName' type='text' value="MGED Ontology" help="the ontology name"/>
            <param name='ontologyFile' type='text' value="http://mged.sourceforge.net/ontologies/MGEDontology.php" help="the ontology file"/>
            <param name='ontologyVersion' type='text' value="1.3.1.1" help="the ontology version"/>
          </when>
          <when value="file">
            <param type="data" format="txt" name="input_yaml" label="Input YAML"/>
          </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="out_idf" label="magetab.idf" from_work_dir="magetab.idf"/>
        <data format="tabular" name="out_sdrf" label="magetab.sdrf" from_work_dir="magetab.sdrf"/>
      </outputs>

    <configfiles>
      <configfile name="idf_yaml"><![CDATA[
#if $params.source == "manual":
expDesign : '$params.expDesign'
expDesignOntology : '$params.expDesignOntology'
expDesignFactorName : '$params.expDesignFactorName'
expDesignFactorType : '$params.expDesignFactorType'
investigationTitle : '$params.investigationTitle'
personLastName : '$params.personLastName'
personFirstName : '$params.personFirstName'
personMidInitial : '$params.personMidInitial'
personEmail : '$params.personEmail'
personAddress : '$params.personAddress'
personAffiliation : '$params.personAffiliation'
personRole : '$params.personRole'
pubMedId : '$params.pubMedId'
pubAuthors : '$params.pubAuthors'
pubTitle : '$params.pubTitle'
pubStatus : '$params.pubStatus'
expDescription : '$params.expDescription'
protocolNames : '$params.protocolNames'
protocolTypes : '$params.protocolTypes'
protocolDescriptions : '$params.protocolDescriptions'
protocolOntologies : '$params.protocolOntologies'
protocolParameters : '$params.protocolParameters'
ontologyName : '$params.ontologyName'
ontologyFile : '$params.ontologyFile'
ontologyVersion : '$params.ontologyVersion'
#end if
]]>
      </configfile>
    </configfiles>

    <help>
usage: python %prog vcfDir protectedIDFFilename protectedSDRFFilename protectedArchiveName openAccessIDFFilename openAccessSDRFFilename openAccessArchiveName [Options]
    </help>
</tool>