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<tool id="seal_read_sort" name="ReadSort" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">
  <description>Sort reads with 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>
    #set $ref_path = 'file://' + $reference.fields.path if $reference.fields.path.startswith('/') else $reference.fields.path
    hadoop_galaxy
    --input $input_data
    --output $output
    --executable seal
    read_sort
    --annotations ${ref_path}.ann
    --num-reducers $num_reducers
  </command>

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

    <param name="reference" type="select" label="Reference (should be the same one used for alignment)">
      <options from_data_table="bwa_0510_indexes" />
    </param>

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

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

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

  <help>
ReadSort is a Hadoop-based program for sorting reads by alignment position.
For the full help see the `manual &lt;http://biodoop-seal.sourceforge.net/read_sort_index.html&gt;`_.
  </help>

</tool>