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  Copyright (C) 2011-2014 CRS4.

  This file is part of Seal.

  Seal is free software: you can redistribute it and/or modify it
  under the terms of the GNU General Public License as published by the Free
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  any later version.

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  for more details.

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<tool id="seal_seqal" name="Seqal" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">
  <description>Map reads 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
    --output $output1
    --executable seal
    seqal
    #if $align_only.value:
      --align-only --num-reducers 0
    #else
      --num-reducers $align_only.num_reducers
    #end if
    --trimq $trimq
    ${reference.fields.path}
  </command>

  <inputs>
    <param name="input_data" type="data" format="pathset" label="Input data" />

    <param name="reference" type="select" label="Select a built-in reference index archive">
      <options from_data_table="seqal_indexes">
      </options>
    </param>

    <param name="trimq" type="integer" min="0" value="0" label="trim quality, like BWA’s -q argument" />

    <conditional name="align_only">
      <param name="value" type="boolean" default="false" label="Align only (don't identify duplicates)" />
      <when value="false">
        <param name="num_reducers"
          label="Number of reduce tasks"
          type="integer"
          value="90"
          min="1"
          />
      </when>
    </conditional>
  </inputs>

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

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

  <help>
    Seqal is a distributed short read mapping and duplicate removal tool. It
    implements a distributed version of the BWA aligner, and adds a duplicate
    read identification feature using the same criteria as the Picard
    MarkDuplicates command.  For a full description see the `manual
    &lt;http://biodoop-seal.sourceforge.net/seqal_index.html&gt;`_.
  </help>
</tool>