<tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="0.2.0">
  <description>for paired data</description>
  <command interpreter="python">
   picard_wrapper.py -i "$input_file" -o "$out_file" --tmpdir "${__new_file_path__}" -n "$out_prefix" 
   --output-format "$outputFormat" -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/FixMateInformation.jar" --sortorder "$sortOrder"
  </command>
  <requirements><requirement type="package">picard</requirement></requirements>
  <inputs>
    <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to fix"
      help="If empty, upload or import a SAM/BAM dataset."/>
      <param name="sortOrder" type="select" help="If in doubt, leave as default and read Picard/Samtools documentation"
         label="Sort order">
        <option value="coordinate" selected ="true">Coordinate sort</option>
        <option value="queryname">Query name sort</option>
        <option value="unsorted">Unsorted - docs not clear if this means unchanged or not</option>
      </param>
    <param name="out_prefix" value="Fix Mate" type="text"
      label="Title for the output file" help="Use this remind you what the job was for." size="80" />
    <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
  </inputs>
  <outputs>
    <data format="bam" name="out_file" label="${tool.name} on ${on_string}: ${outputFormat} with fixed mates">
    <change_format>
     <when input="outputFormat" value="sam" format="sam" />
    </change_format> 
    </data>
  </outputs>
  <tests>
    <test>
      <param name="input_file" value="picard_input_sorted_pair.sam" />
      <param name="sortOrder" value="coordinate" />
      <param name="outputFormat" value="True" />
      <param name="out_prefix" value="Test FixMate" />
      <output name="out_file" file="picard_output_fixmate_sorted_pair.bam" ftype="bam" />
    </test>
    <test>
      <param name="input_file" value="picard_input_sorted_pair.sam" />
      <param name="sortOrder" value="coordinate" />
      <param name="outputFormat" value="False" />
      <param name="out_prefix" value="Test FixMate" />
      <output name="out_file" file="picard_output_fixmate_sorted_pair.sam" ftype="sam" />
    </test>
  </tests>
  <help>


.. class:: infomark

**Purpose**

Ensure that all mate-pair information is in sync between each read and it's mate pair.

**Picard documentation**

This is a Galaxy wrapper for FixMateInformation, a part of the external package Picard-tools_.

 .. _Picard-tools: http://www.google.com/search?q=picard+samtools

.. class:: warningmark

**Useful for paired data only**

Likely won't do anything helpful for single end sequence data
Currently, Galaxy doesn't distinguish paired from single ended SAM/BAM so make sure
the data you choose are valid (paired end) SAM or BAM data - unless you trust this
tool not to harm your data.

-----

.. class:: infomark

**Syntax**

- **Input** - a paired read sam/bam format aligned short read data in your current history
- **Sort order** - can be used to adjust the ordering of reads 
- **Title** - the title to use for all output files from this job - use it for high level metadata
- **Output Format** - either SAM or compressed as BAM

-----

.. class:: infomark

**Inputs, outputs, and parameters**

.. csv-table::

   :header-rows: 1

  Option,Description
  "INPUT=File","The input file to fix. This option may be specified 0 or more times."
  "OUTPUT=File","The output file to write to"
  "SORT_ORDER=SortOrder","Optional sort order if the OUTPUT file should be sorted differently than the INPUT file. Default value: null. Possible values: {unsorted, queryname, coordinate}"
  "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false"

.. class:: warningmark

**Warning on SAM/BAM quality**

Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
to be the only way to deal with SAM/BAM that cannot be parsed.


  </help>
</tool>