muse.xml

<tool id="MuSE" name="MuSE" version="0.9.0">
    <description>variant caller</description>
    <requirements>
        <container type="docker">opengenomics/muse:c039ffa</container>
    </requirements>
    <command interpreter="python">
muse.py
--tumor-bam ${tumor}
--tumor-bam-index ${tumor.metadata.bam_index}
--normal-bam ${normal}
--normal-bam-index ${normal.metadata.bam_index}
-f $reference -w ./
#if $muse.version == "MuSEv0.9.9.5":
-p ${muse.contamination}
#end if
#if $muse.version == "MuSEv1.0rc":
--mode ${muse.mode}
#end if
#if str($dbsnp) != "None"
-D ${dbsnp}
#end if
--cpus \${GALAXY_SLOTS:-4}
-O muse.vcf
--muse ${muse.version}
    </command>
    <inputs>
        <param name="reference" type="data" format="bed, fasta" label="Select a reference genome"/>
        <param name="normal" type="data" format="bam" label="Normal BAM file"/>
        <param name="tumor" type="data" format="bam" label="Tumor BAM file"/>
        <param name="dbsnp" type="data" format="vcf" label="dbsnp.vcf file" optional="true"/>

        <conditional name="muse">
          <param name="version" type="select" label="MuSE Version">
            <option value="MuSEv0.9.9.5" selected="True">MuSEv0.9.9.5</option>
            <option value="MuSEv1.0rc" >MuSEv1.0rc</option>
          </param>
          <when value="MuSEv0.9.9.5">
              <param name="contamination" type="float" value="0.05" help="normal data contamination rate" label="Contamination"/>
          </when>
          <when value="MuSEv1.0rc">
            <param name="mode" type="select" label="BAM Mode">
              <option value="wxs" selected="True">Whole Exome Sequence</option>
              <option value="wgs" >Whole Genome Sequence</option>
            </param>
          </when>
        </conditional>

    </inputs>
    <outputs>
        <data format="vcf" name="mutations" label="MuSE VCF" from_work_dir="muse.vcf"/>
    </outputs>
    <help>

  </help>
</tool>