<!--
  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
  Software Foundation, either version 3 of the License, or (at your option)
  any later version.

  Seal is distributed in the hope that it will be useful, but
  WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
  for more details.

  You should have received a copy of the GNU General Public License along
  with Seal.  If not, see <http://www.gnu.org/licenses/>.
-->


<tool id="dist_bcl2qseq" name="Dist Bcl2Qseq" version="13986416aa79561bd0102cb7ccc1e0668ac9f0a4">
  <description>Convert Illumina bcl files to qseq 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
    --executable seal
    --input $input_data
    --output $output1
    bcl2qseq
    #if $advanced.control == 'show'
      #if $advanced.bcl2qseq_bin:
      --bclToQseq-path $advanced.bcl2qseq_bin
      #end if

      #if $advanced.additional_ld_path
      --append-ld-library-path $advanced.additional_ld_path
      #end if

      #if $advanced.ignore_missing_bcl
      --ignore-missing-bcl
      #end if

      #if $advanced.ignore_missing_control
      --ignore-missing-control
      #end if

      #if $advanced.exclude_controls
      --exclude-controls
      #end if

      #if $advanced.no_eamss
      --no-eamss
      #end if
    #end if
  </command>

  <inputs>
    <param name="input_data" type="data" format="pathset" label="Source data set"/>
    <conditional name="advanced">
      <param name="control" type="select" label="Advanced controls" default="hide">
        <option value="hide">Hide</option>
        <option value="show">Show</option>
      </param>
      <when value="show">
        <param name="ignore_missing_bcl"
          type="boolean" default="false"
          label="Interpret missing *.bcl files as a base calling of '.'"
          />
        <param name="ignore_missing_control"
          type="boolean" default="false"
          label="Don't throw an error when *.control files are missing"
          />
        <param name="exclude_controls"
          type="boolean" default="false"
          label="Do not include clusters that are used as controls"
          />
        <param name="no_eamss"
          type="boolean" default="false"
          label="Do not apply the EAMSS masking on the quality values"
          />
        <param name="bcl2qseq_bin"
          type="text"
          default=""
          size="80"
          label="Full path to bclToQseq binary (needed only if the executable isn't in the PATH)"
          />
        <param name="additional_ld_path"
          type="text" default="" size="80"
          label="paths to append to the value of LD_LIBRARY_PATH"
          />
      </when>
    </conditional>
  </inputs>

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

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

  <help>
    This is a Pydoop-based distributed version of Illumina's bclToQseq tool.
  </help>
</tool>