view pindel.xml @ 6:7f2f81f3644f draft default tip

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<tool id="pindel" name="Pindel" version="0.2.5b8">

  <description>
    a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
  </description>

  <requirements>
    <requirement type="package" version="1.3.2">htslib</requirement>
    <requirement type="package" version="0.2.5b8">pindel</requirement>
  </requirements>

  <command detect_errors="aggressive">

  ln -s $normal normal.bam;
  ln -s $normal.metadata.bam_index normal.bam.bai;
  ln -s $tumour tumour.bam;
  ln -s $tumour.metadata.bam_index tumour.bam.bai;    
 
  touch pindel.txt; 
  #if $sampleid_source.sampleid_selector.value == "bamfile": 
    echo -e \$(pwd)/tumour.bam\\t$normal_insert\\t\$(basename $tumour | rev | cut -c 5- | rev) >> pindel.txt;
    echo -e \$(pwd)/normal.bam\\t$tumour_insert\\t\$(basename $normal | rev | cut -c 5- | rev) >> pindel.txt;
  #else:
    echo -e \$(pwd)/tumour.bam\\t$normal_insert\\t$sampleid_source.idt >> pindel.txt;
    echo -e \$(pwd)/normal.bam\\t$tumour_insert\\t$sampleid_source.idn >> pindel.txt;
  #end if
  
  mkdir outputs;

  #if $reference_source.reference_source_selector.value == "cached":
    ln -s ${reference_source.ref_file.fields.path} ref.fa;
  #else:
    ln -s $reference_source.ref_file ref.fa;
    samtools faidx ref.fa;
  #end if

  pindel
    -f ref.fa
    -i pindel.txt
    -o \$(pwd)/outputs/here
    $advancedsettings.R
    -x $advancedsettings.x 
    -e $advancedsettings.e
    -E $advancedsettings.E
    -u $advancedsettings.u
    -n $advancedsettings.n
    $advancedsettings.r
    $advancedsettings.t
    $advancedsettings.l
    $advancedsettings.k
    $advancedsettings.s
    $advancedsettings.S
    $advancedsettings.I
    #if $advancedsettings.include:
      -j $advancedsettings.include
    #end if
    #if $advancedsettings.exclude:
      -J $advancedsettings.exclude
    #end if
    ;

  first="true";
  for i in \$( ls \$(pwd)/outputs/here* ); do
    pindel2vcf -p \$i -r ref.fa -R CHECK_GALAXY_HISTORY -d CHECK_GALAXY_HISTORY -v tmp.vcf;
    if [ \$first -eq "true" ] ; then
      cat tmp.vcf >> $output;
      first="false";
    else
      grep -v "^#.*" tmp.vcf >> $output;
    fi;
  done;

  </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">
        <param label="Reference Genome File" name="ref_file" type="select">
          <options from_data_table="fasta_indexes"/>
        </param>
      </when>
      <when value="history">
        <param label="Reference Genome File" name="ref_file" type="data" format="fasta"/>
      </when>
    </conditional>

    <conditional name="sampleid_source">
      <param label="Choose the source to open the Sample Id" name="sampleid_selector" type="select">
        <option value="bamfile">BAM File Name</option>
        <option value="manual">Manual</option>
      </param>
      <when value="manual">
        <param name="idt" type="text" label="Tumour ID (Name)"/>
        <param name="idn" type="text" label="Normal ID (Name)"/>
      </when>
    </conditional>

    <param type="data" format="bam" name="tumour" label="Tumour Alignment File"/>
    <param type="data" format="bam" name="normal" label="Normal Alignment File"/>
    <param type="integer" name="tumour_insert" value="250" label="Tumour Insert Size" help="suggest running picards collect insert size metrics"/>
    <param type="integer" name="normal_insert" value="250" label="Normal Insert Size" help="suggest running picards collect insert size metrics"/>

    <section name="advancedsettings" title="Advanced Settings" expanded="false">
      <param type="boolean" name="R" checked="true" truevalue="-R true" falsevalue="-R false" label="Search for Discordant Pairs"/>
      <param type="integer" name="x" value="2" min="1" max="9" label="Maximum size of structural variations to be detected" help="size = 128 ^ (val - 1)"/>
      <param type="float" name="e" value="0.01" max="1.0" label="Expected faraction of sequencing errors"/>
      <param type="float" name="E" value="0.95" max="1.0" label="Sensitivity"/>
      <param type="float" name="u" value="0.02" max="1.0" label="Maximum allowed mismatch rate"/>
      <param type="integer" name="n" value="2" label="Minimum Edit Distance between reads and reference"/>
      <param type="boolean" name="r" checked="true"  truevalue="-r true" falsevalue="-r false" label="Report Inversions"/>
      <param type="boolean" name="t" checked="true"  truevalue="-t true" falsevalue="-t false" label="Report Duplications"/>
      <param type="boolean" name="l" checked="false" truevalue="-l true" falsevalue="-l false" label="Report Long Insertions"/>
      <param type="boolean" name="k" checked="false" truevalue="-k true" falsevalue="-k false" label="Report Breakpoints"/>
      <param type="boolean" name="s" checked="false" truevalue="-s true" falsevalue="-s false" label="Report Close Mapped Reads"/>
      <param type="boolean" name="S" checked="false" truevalue="-S true" falsevalue="-S false" label="Report Only Close Mapped Reads"/>
      <param type="boolean" name="I" checked="false" truevalue="-I true" falsevalue="-I false" label="Report Interchromosomal Events"/>
      <param type="data" format="bed" name="include" label="Include Regions" optional="true"/>
      <param type="data" format="bed" name="exclude" label="Exclude Regions" optional="true"/>
    </section>

  </inputs>

  <outputs>
    <data format="vcf" name="output" />
  </outputs>

</tool>