view somatic_sniper.xml @ 1:2ff18e84c946 draft

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<tool id="somatic_sniper" name="SomaticSniper" version="1.0">
  <description>identify single nucleotide positions that are different between tumor and normal</description>
  <requirements>
    <requirement type="package" version="1.0.5.0">somatic-sniper</requirement>	
  </requirements> 
  <command detect_errors="aggressive"><![CDATA[

  ## SYMLINK BAM FILES ALONGSIDE INDEX FILES
  ln -s $normal normal.bam;
  ln -s $normal.metadata.bam_index normal.bam.bai;
  ln -s $tumor tumor.bam;
  ln -s $tumor.metadata.bam_index tumor.bam.bai;

  #if $interval:

  for i in \$(cut -f1 $interval); do

  #end if

	
  ## BUILD SOMATICSNIPER COMMAND LINE 
  \$CONDA_DEFAULT_ENV/bin/bam-somaticsniper
    -F vcf
    -q $advancedsettings.q
    -Q $advancedsettings.Q
    -T $advancedsettings.T
    -N $advancedsettings.N
    -r $advancedsettings.r
    -n $advancedsettings.n
    -t $advancedsettings.t
    $advancedsettings.L 
    $advancedsettings.G 
    $advancedsettings.p

    #if $ref.ref_options == "cached"
      -f ${ref.index.fields.path}
    #else
      -f ${ref.ownFile}
    #end if

    #if $interval:
    
    <(samtools view -b tumor.bam \$i)
    <(samtools view -b normal.bam \$i)
    
    #else:
      tumor.bam
      normal.bam

    #end if

    #if $interval:
      tmp_\$i.txt
    #else:
      $variants
    #end if
    ;

    #if $interval:

      done;
    
      for i in \$(cut -f1 $interval); do
      
      if [ \$i == \$(cut -f1 $interval | head -n1) ] ; then
        cat tmp_\$i.txt > $variants;
      else
        grep -v ^#.* tmp_\$i.txt >> $variants;
      fi ;

      done;  

    #end if



    ]]></command>
	<inputs>
		<conditional name="ref">
			<param name="ref_options" type="select" label="Choose the source for the reference genome">
				<option value="cached" selected="True">Use a built-in genome</option>
				<option value="history">Use a genome from the history</option>
			</param>
			<when value="cached">
				<param name="index" type="select" label="Reference Genome File" >
					<options from_data_table="all_fasta" />
				</param>
      			</when>
      			<when value="history">
        			<param format="fasta" name="ownFile" type="data" metadata_name="dbkey" label="Reference Genome File" />
      			</when>
		</conditional>
		<param format="bam" name="normal" type="data" label="Normal Alignment File" />
		<param format="bam" name="tumor" type="data" label="Tumour Alignment File" />
                <param type="data" format="txt" optional="true" name="interval" label="Specify Inteval"/>
		<section name="advancedsettings" title="Advanced Settings" expanded="False" >
			<param name="q" type="integer" value="0" label="Minimum read mapping quality"/>
			<param name="Q" type="integer" value="15" label="Minimum somatic variant quality score"/>
			<param name="T" type="float" value="0.850000" label="theta in maq consensus calling model (for -c/-g) [0.850000]"/>
			<param name="N" type="integer" value="2" label="Ploidy (number of haplotypes)"/>
			<param name="r" type="float" value="0.001000" label="Prior probability for differences between haplotypes"/>
			<param name="n" type="text" value="NORMAL" label="Normal sample ID"/>
			<param name="t" type="text" value="TUMOR" label="Tumour sample ID"/>
  			<param name="L" type="boolean" truevalue="-L" falsevalue="" checked="true" label="Exclude LOH variants from output" />
  			<param name="G" type="boolean"  truevalue="-G" falsevalue="" checked="true" label="Exclude gain of reference variants from output" />
  			<param name="p" type="boolean"  truevalue="-p" falsevalue="" checked="true" label="Disable priors in somatic calculation (improved sensitivity for solid tumours)" />
		</section>
	</inputs>
	<outputs>
		<data name="variants" format="vcf" label="SomaticSniper SNVs" />
	</outputs>
	<tests>
                <test>
                  <param name="normal" file="sniper_test_normal.bam" />
                  <param name="tumor" file="sniper_test_tumoral.bam" />
                  <output name="variants" file="sniper_results.vcf" />
                </test>
        </tests>
	<help>
		http://gmt.genome.wustl.edu/packages/somatic-sniper/
	</help>
</tool>