view create_seqz_file.xml @ 3:235c8e5dfece draft default tip

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<tool id="create_seqz_file" name="Create Seqz File" version="2.1.2">
<description>
    extracts the common positions containing A and B allele frequencies
</description>
<requirements>
  <requirement type="package" version="2.1.2">sequenza</requirement>
  <requirement type="package" version="5.4.1">pypy</requirement>
  <requirement type="set_environment" version="2.1.2">SEQUENZA_INSTALL_DIR</requirement>
</requirements>
<command><![CDATA[

    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;
  

    #if $reference_source.reference_source_selector == "history":
      ln -s $reference_source.ref_file reference.fa;
      samtools faidx reference.fa;
    #elif $reference_source.reference_source_selector == "cached":
      ln -s ${reference_source.ref_file.fields.path} reference.fa;	
    #end if

    EXEC=python;
    if [ \$(which pypy)!="" ] ; then
      EXEC=pypy;
    fi ;

    #if $interval
      #if $gzip.gzip_selector == "yes"
        echo 1 >> $bytes;
      #end if
      for int in \$( cat $interval ); do
    #end if

    #if $interval and $order_file
      if [ "\$int" != "\$( cat $order_file | head -n1)" ] ; then
        skip=2;
      else
        skip=1;
      fi ;
    #end if

    \$EXEC \$SEQUENZA_INSTALL_DIR/sequenza/exec/sequenza-utils.py bam2seqz 
      -n normal.bam 
      -t tumour.bam
      -gc $gc_file
      -F reference.fa 

      #if $interval
        -C \$int
      #end if

      --hom $geno.hom
      --het $geno.het
      -q $qual.qlimit
      -f $qual.qformat
      -N $qual.depth
      
    | \$EXEC \$SEQUENZA_INSTALL_DIR/sequenza/exec/sequenza-utils.py seqz-binning
      -s -
      -w $window
    
    | awk '{ if (\$4 >= $min_depth && \$5 >= $min_depth) print \$_ }'
      
    #if $gzip.gzip_selector == "yes":
      #if $order_file and $interval:
        | tail -n+\$skip | gzip >> $output_gzip;
      #else
        | gzip >> $output_gzip;
      #end if

      #if $interval:
        echo \$(( \$( wc -c < $output_gzip ) + 1 )) >> $bytes;
      #end if

    #else:
      >> $output;
    #end if
      
    #if $interval
      done;
    #end if
  
]]></command>
<inputs>
<conditional name="reference_source">
<param label="Choose the source for the reference files" name="reference_source_selector" type="select">
<option value="cached">Locally Cached</option>
<option value="history">History</option>
</param>
<when value="cached">
<param label="Genome" name="ref_file" type="select">
<options from_data_table="fasta_indexes"/>
</param>
</when>
<when value="history">
<param label="Genome" name="ref_file" type="data" format="fasta"/>
</when>
</conditional>
<param name="normal" label="Normal Alignment File (BAM)" type="data" format="data"/>
<param name="tumour" label="Tumour Alignment File (BAM)" type="data" format="data"/>
<param label="GC Window File" name="gc_file" type="data" format="tabular"/>
<param label="Bin Output by Window" name="window" type="integer" min="1" max="50" value="50"/>
<param name="min_depth" label="Minimum coverage for variant to be used in model" type="integer" min="1" max="50" value="12"/>
    <conditional name="gzip">
      <param label="Should the output be gzipped" name="gzip_selector" type="select">
        <option value="yes" selected="true">Yes</option>
        <option value="no">No</option>
      </param>
    </conditional>
    <param name="interval" optional="true" label="Restrict Computation to a particular Interval" help="Must be present in the BAM" 
type="data" format="txt"/>
<param name="order_file" optional="true" label="Order File" help="Should be Present with Interval File" type="data" format="txt"/>
    <section name="geno" title="Genotyping Options" expanded="False">
<param name="hom" label="Threshold to Select Homozygous Positions" type="float" value="0.9" min="0" max="1"/>
<param name="het" label="Threshold to Select Heterozygous Positions" type="float" value="0.25" min="0" max="1"/>
</section>
<section name="qual" title="Quality Threshold Options" expanded="False">
<param name="depth" label="Treshold to Filter Positions" help="The sum of read depth in both samples" value="20" type="integer"/>
<param name="qlimit" label="Minimum Nucleotide Quality Score" value="20" type="integer"/>
<param name="qformat" label="Quality Format" type="select">
<option value="sanger">Sanger</option>
<option value="illumina">Illumina</option>
</param>
</section>
</inputs>
<outputs>
<data format="tabular" name="output" label="Seqz File">
      <filter>gzip['gzip_selector'] == "no"</filter>
    </data>
    <data format="txt" name="output_gzip" label="Gzipped Seqz File">
      <filter>gzip['gzip_selector'] == "yes"</filter>
    </data>
    <data format="txt" name="bytes" label="Gzip Block Locations">
      <filter>gzip['gzip_selector'] == "yes"</filter>
    </data>
</outputs>
</tool>