view sequenza_pipeline.xml @ 2:12d83c22866a draft

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<tool id="sequenza_pipeline" name="Analyze Seqz File" version="2.1.2">
  <description>
  using general R sequenza pipeline
  </description>
  <requirements>
    <requirement type="package" version="2.1.2">sequenza</requirement>
    <requirement type="set_environment" version="2.1.2">SEQUENZA_INSTALL_DIR</requirement>
  </requirements>
<command>

Rscript $__tool_directory__/sequenza_pipeline.R $input

    #if $sampleid_source.sampleid_selector == "bamfile":
      \$(basename $sampleid_source.id | sed 's/.bam$//g' )
    #else:
      $sampleid_source.id
    #end if

    output
    
    #if $choose_fit_option.fit_option == "manual":
    
      $ploidy $cellularity
    
    #end if
     
    2>&amp;1 ;

  cat ./output/*segments.txt > $output;

  </command>
<inputs>
    <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="id" type="text" label="Tumour ID (Name)"/>
      </when>
      <when value="bamfile">
        <param type="data" format="bam" name="id" label="Sequence Alignment File"/>
      </when>
    </conditional>
    <conditional name="choose_fit_option">
    <param label="Use the best fit or manually set the ploidy and cellularity" name="fit_option" type="select">
      <option value="bestfit">Best fit</option>
      <option value="manual">Manually specify</option>
    </param>
    <when value="manual">
      <param name="ploidy" type="float" label="ploidy" value="2" />
      <param name="cellularity" type="float" label="cellularity" value="1" />
    </when>
    </conditional>
    <param name="input" format="txt,tabular" type="data" label="Input Sequenza Seqz File"/>
  </inputs>
  <outputs>
    <data name="output" format="seg,txt"/>
    <collection name="list_output" type="list" description="Sequenza outputs">
      <discover_datasets pattern="__name_and_ext__" directory="output"/>
    </collection> 
  </outputs>
</tool>