radia_filter.xml

<tool id="radia_filter" name="radia_filter" version="0.1.0">
    <macros>
      <macro name="input_params">
        <param name="inputbam" label="InputBam" type="data" format="bam" help="Input BAM"/>
        <conditional name="fasta">
        <param name="use" type="select" label="Use different fasta">
          <option value="yes">yes</option>
          <option value="no" selected="True">no</option>
        </param>
        <when value="yes">
          <param name="inputfasta" label="Fasta file used to create Bam file (if different from top)" type="data" format="fasta" help="Fasta file used to create this bam file"/>
        </when>
      </conditional>
      </macro>
      <macro name="input_filter">
        <param name="filterfile" label="InputFile" type="data" format="bed" help="Input coordinate file"/>
      </macro>
    </macros>
    <requirements>
      <container type="docker">radia:1.1.5</container>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command interpreter="python"><![CDATA[
radia_filter.py

--outputFilename out.vcf
#if $patientId:
--patientId ${patientId}
#end if
--inputVCF ${inputVCF}
--fastaFilename ${inputFasta}
#if $tcga:
--makeTCGAcompliant
#end if

#if $filterRejects:
--filter-rejects
#end if

#if $filterGermline:
--filter-germline
#end if

## params for normal DNA
#if $dnaNormal.use == "yes":
--dnaNormalFilename ${dnaNormal.inputbam}
--dnaNormalBaiFilename ${dnaNormal.inputbam.metadata.bam_index}
#if $dnaNormal.fasta.use == "yes"
--dnaNormalFastaFilename ${dnaTumor.fasta.inputfasta}
#end if
#end if

## params for tumor DNA
#if $dnaTumor.use == "yes":
--dnaTumorFilename ${dnaTumor.inputbam}
--dnaTumorBaiFilename ${dnaTumor.inputbam.metadata.bam_index}
#if $dnaTumor.fasta.use == "yes"
--dnaTumorFastaFilename ${dnaTumor.fasta.inputfasta}
#end if
#end if

## params for normal RNA
#if $rnaNormal.use == "yes":
--rnaNormalFilename ${rnaNormal.inputbam}
--rnaNormalBaiFilename ${rnaNormal.inputbam.metadata.bam_index}
#end if

## params for tumor RNA
#if $rnaTumor.use == "yes":
--rnaTumorFilename ${rnaTumor.inputbam}
--rnaTumorBaiFilename ${rnaTumor.inputbam.metadata.bam_index}
#if $rnaTumor.blat.useBlat == "yes":
--blatFastaFilename ${rnaTumor.blat.filterfile}
${rnaTumor.blat.positional}
#end if
#end if

## filters
#if $blacklist.use == "yes":
--blacklistFilename ${blacklist.filterfile}
#end if
#if $target.use == "yes":
--targetFilename ${target.filterfile}
#end if
#if $dbsnp.use == "yes":
--snpFilename ${dbsnp.filterfile}
#end if
#if $retrogenes.use == "yes":
--retroGenesFilename ${retrogenes.filterfile}
#end if
#if $pseudogenes.use == "yes":
--pseudoGenesFilename ${pseudogenes.filterfile}
#end if
#if $cosmic.use == "yes":
--cosmicFilename ${cosmic.filterfile}
#end if
#if $snpeff.use == "yes":
--snpEffFilename ${snpeff.zipfile}
${snpeff.canonical}
--snpEffDir /opt/snpEff
#if $snpeff.rnaBlacklist.useRB == "yes":
--rnaGeneBlckFile ${snpeff.rnaBlacklist.rnaBlacklistFile}
--rnaGeneFamilyBlckFile ${snpeff.rnaBlacklist.rnaBlacklistFamily}
#end if
#end if

--outputDir ./
--scriptsDir /opt/radia-1.1.5/scripts/
--number_of_procs \${GALAXY_SLOTS:-1}

    ]]></command>
    <inputs>

      <param name="patientId" label="Patient ID" type="text" value="MyPatient" help=""/>
      <param name="inputVCF" label="Radia VCF" type="data" format="vcf" help="Radia output vcf file"/>
      <param name="inputFasta" label="Universal fasta file used to create Bam files" type="data" format="fasta" help="Fasta file used to create all Bam files"/>
      <param name="tcga" type="boolean" label="format for TCGA submission?" checked="true"/>
      <param name="filterRejects" type="boolean" label="Filter Rejected calls" checked="true"/>
      <param name="filterGermline" type="boolean" label="Filter Germline calls" checked="true"/>


      <conditional name="dnaNormal">
        <param name="use" type="select" label="Use DNA Normal">
          <option value="yes">yes</option>
          <option value="no" selected="True">no</option>
        </param>
        <when value="yes">
          <expand macro="input_params"/>
        </when>
      </conditional>

      <conditional name="dnaTumor">
        <param name="use" type="select" label="Use DNA Tumor">
          <option value="yes">yes</option>
          <option value="no" selected="True">no</option>
        </param>
        <when value="yes">
          <expand macro="input_params"/>
        </when>
      </conditional>

      <conditional name="rnaNormal">
        <param name="use" type="select" label="Use RNA Normal">
          <option value="yes">yes</option>
          <option value="no" selected="True">no</option>
        </param>
        <when value="yes">
          <expand macro="input_params"/>
        </when>
      </conditional>

      <conditional name="rnaTumor">
        <param name="use" type="select" label="Use RNA Tumor">
          <option value="yes">yes</option>
          <option value="no" selected="True">no</option>
        </param>
        <when value="yes">
          <expand macro="input_params"/>
          <conditional name="blat"> 
              <param name="useBlat" type="select" label="Use blat filter">
                <option value="yes">yes</option>
                <option value="no" selected="True">no</option>
              </param>
              <when value="yes">
                  <param name="filterfile" label="InputFile" type="data" format="fasta" help="Genome fasta file for blat"/>
                  <param name="positional" type="boolean" truevalue="--noPositionalBias" falsevalue="" label="Use positional bias?"/>
              </when>
          </conditional>
        </when>
      </conditional>

      <conditional name="blacklist">
        <param name="use" type="select" label="Use blacklist filter">
          <option value="yes">yes</option>
          <option value="no" selected="True">no</option>
        </param>
        <when value="yes">
          <expand macro="input_filter"/>
        </when>
      </conditional>

      <conditional name="target">
        <param name="use" type="select" label="Use exon capture targets">
          <option value="yes">yes</option>
          <option value="no" selected="True">no</option>
        </param>
        <when value="yes">
          <expand macro="input_filter"/>
        </when>
      </conditional>

      <conditional name="dbsnp">
        <param name="use" type="select" label="Use SNP filter">
          <option value="yes">yes</option>
          <option value="no" selected="True">no</option>
        </param>
        <when value="yes">
          <param name="filterfile" label="InputFile" type="data" format="vcf" help="dbSNP vcf file"/>
        </when>
      </conditional>

      <conditional name="retrogenes">
        <param name="use" type="select" label="Use retrogenes filter">
          <option value="yes">yes</option>
          <option value="no" selected="True">no</option>
        </param>
        <when value="yes">
          <expand macro="input_filter"/>
        </when>
      </conditional>

      <conditional name="pseudogenes">
        <param name="use" type="select" label="Use pseudogenes filter">
          <option value="yes">yes</option>
          <option value="no" selected="True">no</option>
        </param>
        <when value="yes">
          <expand macro="input_filter"/>
        </when>
      </conditional>

      <conditional name="cosmic">
        <param name="use" type="select" label="Use Catalogue Of Somatic Mutations In Cancer (COSMIC) annotation filter">
          <option value="yes">yes</option>
          <option value="no" selected="True">no</option>
        </param>
        <when value="yes">
          <expand macro="input_filter"/>
        </when>
      </conditional>

      <conditional name="snpeff">
        <param name="use" type="select" label="Use snpEff to annotate VCF">
          <option value="yes">yes</option>
          <option value="no" selected="True">no</option>
        </param>
        <when value="yes">
           <param name="zipfile" label="inputFile" type="data" format="snpeffdb" help="SnpEff zipped input file"/>
           <param name="canonical" type="boolean" truevalue="--canonical" falsevalue="" label="use only canonical transcripts"/>
           <conditional name="rnaBlacklist">
             <param name="useRB" type="select" label="Use blacklist of RNA IDs">
               <option value="yes">yes</option>
               <option value="no" selected="True">no</option>
             </param>
             <when value="yes">
               <param name="rnaBlacklistFile" label="RNA gene inputFile" type="data" help="List of RNA IDs"/>
               <param name="rnaBlacklistFamily" label="RNA family inputFile" type="data" help="List of RNA family IDs"/>
             </when>
           <param name="zipfile" label="inputFile" type="data" format="snpeffdb" help="SnpEff zipped input file"/>
           <param name="canonical" type="boolean" truevalue="--canonical" falsevalue="" label="use only canonical transcripts"/>
           </conditional>
        </when>
      </conditional>

    </inputs>
    <outputs>
      <data name="output_vcf" format="vcf" from_work_dir="out.vcf"/>
    </outputs>
    <help><![CDATA[
        TODO: Fill in help.
    ]]></help>
</tool>