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<tool id="seal_recab_table" name="Recab Table" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">
  <description>Calculate a base quality recalibration table 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 interpreter="python">
    recab_table_galaxy.py
    $input_data
    $output1
   
    #if $dbsnp.db_source == "history":
        $dbsnp.ownFile
    #else:
        ${dbsnp.built-inFile.fields.path} 
    #end if

    $num_reducers

    #if $default_rg:
    -D seal.recab.rg-covariate.default-rg=$default_rg
    #end if

    #if $smoothing:
    -D seal.recab.smoothing=$smoothing
    #end if 

    #if $max_qscore:
    -D seal.recab.max-qscore=$max_qscore
    #end if
  </command>

  <inputs>
    <param name="input_data" type="data" format="pathset" label="Input data" />
    <param name="input_format" type="select" label="Input format" default="sam">
      <option value="sam" />
      <option value="bam" />
    </param>

    <conditional name="dbsnp"> 
      <param name="db_source" type="select" label="Select database of known variation sites">        
        <option value="built-in">Select a different built-in database</option>
        <option value="history">Use a database (vcf format) from my history</option>
      </param>       

        <when value="built-in">
        <param name="built-inFile" type="select" label="Select a built-in database">
          <options from_data_table="variant_tables"/>
        </param>
      </when>

      <when value="history">
        <param name="ownFile" type="data" format="vcf" label="Select a database from history"/>
      </when>
    </conditional>


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

    <!-- recab-specific parameters -->
    <param name="default_rg"
      label="Default read group"
      type="text"
      help="Read group to assign to mappings without an RG tag. This value is mandatory if your data includes mappings that do not have a read group tag (RG) Seal RecabTable property: seal.recab.rg-covariate.default-rg."
      />
    <param name="smoothing"
      label="Smoothing"
      type="integer"
      value="0"
      help="Smoothing parameter for empirical quality calculation. Seal RecabTable property: seal.recab.smoothing."
      min="0"
      />
    <param name="max_qscore"
      label="Max quality score"
      type="integer"
      value="40"
      min="1"
      help="Upper limit for the empirical quality scores. Seal RecabTable property: seal.recab.max-qscore."
      />
  </inputs>

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

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

  <help>
RecabTable is a Hadoop program to calculate a table of base qualities for all values of a given set of factors. It computes a result equivalent to the GATK CountCovariatesWalker.
For the full help see the `manual &lt;http://biodoop-seal.sourceforge.net/recab_table_index.html&gt;`_.
  </help>
</tool>