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<tool id="seal_merge_alignments" name="Merge Alignments" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">
  <description>Merge a pathset of part-files of alignments into a single well-formatted SAM file</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 interpreter="python">
    #set $ref_path = 'file://' + $reference.fields.path if $reference.fields.path.startswith('/') else $reference.fields.path
    merge_alignments.py
    $input_data
    $output

    --annotations ${ref_path}.ann
    --sort-order $sort_order

    #if $compute_md5:
    --md5
    #end if

    #if $assembly:
    --sq-assembly "$assembly"
    #end if

    #if $rg.set_rg == 'true':
      --rg_cn "$rg.rg_cn"
      --rg_dt "$rg.rg_dt"
      --rg_id "$rg.rg_id"
      --rg_lb "$rg.rg_lb"
      --rg_pl "$rg.rg_pl"
      --rg_pu "$rg.rg_pu"
      --rg_sm "$rg.rg_sm"
    #end if
  </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="sort_order" type="select" default="coordinate">
      <option value="coordinate">Coordinate</option>
      <option value="read_id">Read ID</option>
      <option value="unsorted">Unsorted</option>
    </param>
    <param name="compute_md5" type="boolean" checked="false" label="Whether to compute the MD5 checksums of the reference contigs" />
    <param name="assembly" type="text" label="Genome assembly identifier (@SQ AS:XXX tag)" />

    <conditional name="rg">
      <param name="set_rg" type="boolean" checked="false" label="Set a Read Group line" truevalue="true" falsevalue="false" />

      <when value="true">
        <param name="rg_cn" type="text" label="Read group center" />
        <param name="rg_dt" type="text" label="Read group date" />
        <param name="rg_id" type="text" label="Read group id" />
        <param name="rg_lb" type="text" label="Read group library" />
        <param name="rg_pl" type="text" label="Read group platform" />
        <param name="rg_pu" type="text" label="Read group platform unit" />
        <param name="rg_sm" type="text" label="Read group sample" />
      </when>
    </conditional>
  </inputs>

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