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  This file is part of Seal.

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<tool id="seal_prq" name="Prq" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">
  <description>Convert qseq or fastq files to prq on Hadoop</description>
  <requirements>
    <requirement type="package" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">seal</requirement>
    <requirement type="package" version="0.11">pydoop</requirement>
    <requirement type="package" version="0.1.3">hadoop-galaxy</requirement>
  </requirements>
  <command>
    hadoop_galaxy
    --input $input_data
    --input-format $input_format.type
    --output $output1
    --executable seal
    prq
    --input-format $input_format.type
    --num-reducers $num_reducers
    -D hbam.qseq-input.base-quality-encoding=$input_format.bq_encoding
    -D hbam.fastq-input.base-quality-encoding=$input_format.bq_encoding

    #if $bpr
      -D seal.prq.min-bases-per-read=$bpr
    #end if
    #if $drop_failed
      -D seal.prq.drop-failed-filter=$drop_failed
    #end if
    #if $warn_unpaired
      -D seal.prq.warning-only-if-unpaired=$warn_unpaired
    #end if
  </command>

  <inputs>
    <param name="input_data" type="data" format="pathset" label="Input data" />
    <conditional name="input_format">
      <!-- We use a conditional for the input_format since we want a different
           default base quality encoding value for each of the respective
           supported formats, qseq and fastq.-->
      <param name="type" type="select" label="Input format" default="qseq">
        <option value="qseq" />
        <option value="fastq" />
      </param>
      <when value="qseq">
        <param name="bq_encoding" type="select" label="BQ encoding" default="illumina">
          <option value="illumina">Illumina</option>
          <option value="sanger">Sanger</option>
        </param>
      </when>
      <when value="fastq">
        <param name="bq_encoding" type="select" label="BQ encoding" default="sanger">
          <option value="sanger">Sanger</option>
          <option value="illumina">Illumina</option>
        </param>
      </when>
    </conditional>

    <param name="num_reducers"
      label="Number of reduce tasks"
      type="integer"
      value="90"
      min="1"
      />

    <!-- prq-specific parameters -->
    <param name="bpr"
      label="Min bases per read"
      type="integer"
      help="If neither read in a pair has at least this many known bases the pair is dropped (prop: seal.prq.min-bases-per-read)."
      value="30"
      min="0"
      />
    <param name="drop_failed"
      label="Filter by machine quality check"
      type="boolean"
      help="Drop pairs if both reads failed machine quality checks (prop: seal.prq.drop-failed-filter)."
      checked="true"
      />
    <param name="warn_unpaired"
      label="Warn only on unpaired reads"
      type="boolean"
      help="PRQ normally gives an error if it finds an unpaired read. If this setting is checked it will instead emit a warning, drop the unpaired read and keep going (prop: seal.prq.warning-only-if-unpaired)."
      checked="false"
      />
  </inputs>

  <outputs>
    <data name="output1" format="pathset" />
  </outputs>

  <stdio>
    <exit_code range="1:" level="fatal" />
  </stdio>

  <help>
PairReadsQSeq (PRQ) is a Hadoop utility to convert  Illumina qseq files into
prq file format.  For the full help see the `manual &lt;http://biodoop-seal.sourceforge.net/prq_index.html&gt;`_.
  </help>

</tool>