radia.xml

<tool id="radia" name="radia" version="0.1.0">
    <requirements>
      <container type="docker">radia:1.1.5</container>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command interpreter="python"><![CDATA[
radia.py

--outputFilename out.vcf
#if $patientId:
--patientId ${patientId}
#end if
--fastaFilename ${fastaFile}
--refId "${refId}"
--refUrl "${refUrl}"
--dataSource "${dataSource}"
--sequencingPlatform "${sequencingPlatform}"
--statsDir stats
--disease "${disease}"

--genotypeMinDepth ${genotypeMinDepth}
--genotypeMinPct ${genotypeMinPct}

## params for normal DNA
#if $dnaNormal.use == "yes":
--dnaNormalFilename ${dnaNormal.dn_inputbam}
--dnaNormalBaiFilename ${dnaNormal.dn_inputbam.metadata.bam_index}
#if $dnaNormal.fasta.use == "yes"
--dnaNormalFasta ${dnaNormal.fasta.inputfasta}
#end if
--dnaNormalMinTotalBases ${dnaNormal.MinTotalBases}
--dnaNormalMinAltBases ${dnaNormal.MinAltBases}
--dnaNormalBaseQual ${dnaNormal.MinBaseQuality}
--dnaNormalMapQual ${dnaNormal.MinMappingQuality}
--dnaNormalDescription "${dnaNormal.Description}"
#end if

## params for normal RNA
#if $rnaNormal.use == "yes":
--rnaNormalFilename ${rnaNormal.rn_inputbam}
--rnaNormalBaiFilename ${rnaNormal.rn_inputbam.metadata.bam_index}
#if $rnaNormal.fasta.use == "yes"
--rnaNormalFasta ${rnaNormal.fasta.inputfasta}
#end if
--rnaNormalMinTotalBases ${rnaNormal.MinTotalBases}
--rnaNormalMinAltBases ${rnaNormal.MinAltBases}
--rnaNormalBaseQual ${rnaNormal.MinBaseQuality}
--rnaNormalMapQual ${rnaNormal.MinMappingQuality}
--rnaNormalDescription "${rnaNormal.Description}"
#end if


## params for tumor DNA
#if $dnaTumor.use == "yes":
--dnaTumorFilename ${dnaTumor.dt_inputbam}
--dnaTumorBaiFilename ${dnaTumor.dt_inputbam.metadata.bam_index}
#if $dnaTumor.fasta.use == "yes"
--dnaTumorFasta ${dnaTumor.fasta.inputfasta}
#end if
--dnaTumorMinTotalBases ${dnaTumor.MinTotalBases}
--dnaTumorMinAltBases ${dnaTumor.MinAltBases}
--dnaTumorBaseQual ${dnaTumor.MinBaseQuality}
--dnaTumorMapQual ${dnaTumor.MinMappingQuality}
--dnaTumorDescription "${dnaTumor.Description}"
#end if

## params for tumor RNA
#if $rnaTumor.use == "yes":
--rnaTumorFilename ${rnaTumor.rt_inputbam}
--rnaTumorBaiFilename ${rnaTumor.rt_inputbam.metadata.bam_index}
#if $rnaTumor.fasta.use == "yes"
--rnaTumorFasta ${rnaTumor.fasta.inputfasta}
#end if
--rnaTumorMinTotalBases ${rnaTumor.MinTotalBases}
--rnaTumorMinAltBases ${rnaTumor.MinAltBases}
--rnaTumorBaseQual ${rnaTumor.MinBaseQuality}
--rnaTumorMapQual ${rnaTumor.MinMappingQuality}
--rnaTumorDescription "${rnaTumor.Description}"
#end if

--outputDir ./
--scriptsDir /opt/radia-1.1.5/scripts/
--number_of_procs \${GALAXY_SLOTS:-1}
    ]]></command>
    <inputs>
      <param name="patientId" label="Patient ID (no spaces)" type="text" value="Patient" help="Patient's unique ID number"/>
      <param name="fastaFile" label="Reference Genome" type="data" format="fasta" help="Fasta file used for read alignments"/>
      <param name="refId" label="Reference Genome ID" type="text" value="hg19" help="Genome used for read alignments"/>
      <param name="refUrl" label="Reference Genome URL" type="text" value="" help="URL for genome fasta file(s)"/>
      <param name="dataSource" label="Data Source" type="text" value="" help="Original location of bam files"/>
      <param name="sequencingPlatform" label="SequencingPlatform" type="text" value="" help="E.g. Illumina"/>
      <param name="disease" label="Disease Code" type="text" value="" help="Short disease code such as BRCA or LGG"/>

      <param name="genotypeMinDepth" label="genotypeMinDepth" type="integer" value="2" help="the minimum number of bases required for the genotype"/>
      <param name="genotypeMinPct" label="genotypeMinPct" type="float" value=".10" help="the minimum percentage of reads required for the genotype"/>

      <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">
          <param name="dn_inputbam" label="DNA Normal 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>
          <param name="MinTotalBases" label="MinTotalBases" type="integer" value="4" help="the minimum number of overall reads covering a position"/>
          <param name="MinAltBases" label="MinAltBases" type="integer" value="2" help="the minimum number of alternative reads supporting a variant at a position"/>
          <param name="MinBaseQuality" label="MinBaseQuality" type="integer" value="10" help="the minimum base quality"/>
          <param name="MinMappingQuality" label="MinMappingQuality" type="integer" value="10" help="the minimum mapping quality"/>
          <param name="Description" label="Description" value="NormalDNASample" type="text" help="the single word description for the sample in the VCF header"/>
        </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">
          <param name="dt_inputbam" label="DNA Tumor 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>
          <param name="MinTotalBases" label="MinTotalBases" type="integer" value="4" help="the minimum number of overall reads covering a position"/>
          <param name="MinAltBases" label="MinAltBases" type="integer" value="2" help="the minimum number of alternative reads supporting a variant at a position"/>
          <param name="MinBaseQuality" label="MinBaseQuality" type="integer" value="10" help="the minimum base quality"/>
          <param name="MinMappingQuality" label="MinMappingQuality" type="integer" value="10" help="the minimum mapping quality"/>
          <param name="Description" label="Description" value="NormalDNASample" type="text" help="the single word description for the sample in the VCF header"/>
        </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">
          <param name="rn_inputbam" label="RNA Normal 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>
          <param name="MinTotalBases" label="MinTotalBases" type="integer" value="4" help="the minimum number of overall reads covering a position"/>
          <param name="MinAltBases" label="MinAltBases" type="integer" value="2" help="the minimum number of alternative reads supporting a variant at a position"/>
          <param name="MinBaseQuality" label="MinBaseQuality" type="integer" value="10" help="the minimum base quality"/>
          <param name="MinMappingQuality" label="MinMappingQuality" type="integer" value="10" help="the minimum mapping quality"/>
          <param name="Description" label="Description" value="NormalDNASample" type="text" help="the single word description for the sample in the VCF header"/>
        </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">
          <param name="rt_inputbam" label="RNA Tumor 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>
          <param name="MinTotalBases" label="MinTotalBases" type="integer" value="4" help="the minimum number of overall reads covering a position"/>
          <param name="MinAltBases" label="MinAltBases" type="integer" value="2" help="the minimum number of alternative reads supporting a variant at a position"/>
          <param name="MinBaseQuality" label="MinBaseQuality" type="integer" value="10" help="the minimum base quality"/>
          <param name="MinMappingQuality" label="MinMappingQuality" type="integer" value="10" help="the minimum mapping quality"/>
          <param name="Description" label="Description" value="NormalDNASample" type="text" help="the single word description for the sample in the VCF header"/>
        </when>
      </conditional>
    </inputs>
    <outputs>
      <data name="output_vcf" format="vcf" from_work_dir="out.vcf"/>
    </outputs>
    <help><![CDATA[
        TODO: Fill in help.
    ]]></help>
</tool>