<tool id="extractSplitReads_BwaMem"
      name="Extract Split Reads"
      version="0.1.0">

    <description>from bwaMEM (part of lumpy-sv)</description>

    <requirements>
        <requirement type="package" version="0.2.14a">lumpy-sv</requirement>
    </requirements>

    <version_command>extractSplitReads_BwaMem | grep ^extractSplitReads_BwaMem | cut -d v -f 2</version_command>

    <command detect_errors="aggressive">
        <![CDATA[
            extractSplitReads_BwaMem
            -i '$input'
            -n $numSplits
            $includeDups
            -m $minNonOverlap
            > '$output'
        ]]>
    </command>

    <inputs>

        <param format="sam" name="input" type="data" label="Sam alignment file" argument="--infile"/>

        <param name="numSplits"
               label="numSplits"
               argument="--numSplits"

               type="integer"
               value="2"

               help="The maximum number of split-read mappings to allow per read. Reads with more are excluded." />

        <param name="includeDups"
               label="includeDups"
               argument="--includeDups"

               type="boolean"
               truevalue="--includeDups"
               falsevalue=""
               checked="no"
               value="false"

               help="Include alignments marked as duplicates." />

        <param name="minNonOverlap"
               label="minNonOverlap"
               argument="--minNonOverlap"

               type="integer"
               value="20"

               help="Minimum non-overlap between split alignments on the query." />

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

    <tests>
        <test>
            <param name="input" value="JS01-BWA-MEM.splitters.sam"/>
            <output name="output" file="JS01-BWA-MEM.splitters.out.sam"/>
        </test>
        <test>
            <param name="input" value="pe.pos_sorted.sam"/>
            <output name="output" file="pe.pos_sorted.out.sam"/>
        </test>
    </tests>

    <help>
        <![CDATA[

Usage: `extractSplitReads_BwaMem -i <file>`

extractSplitReads_BwaMem v0.1.0

Author: Ira Hall

Description: Get split-read alignments from bwa-mem in lumpy compatible format. Ignores reads marked as duplicates.

Works on read or position sorted SAM input. Tested on bwa mem v0.7.5a-r405. 


Options:
  -h, --help            show this help message and exit
  -i FILE, --inFile=FILE
                        A SAM file or standard input (-i stdin).
  -n INT, --numSplits=INT
                        The maximum number of split-read mappings to allow per
                        read. Reads with more are excluded. Default=2
  -d, --includeDups     Include alignments marked as duplicates. Default=False
  -m INT, --minNonOverlap=INT
                        minimum non-overlap between split alignments on the
                        query (default=20)

        ]]>
    </help>

    <citations>
        <citation type="doi">doi:10.1186/gb-2014-15-6-r84</citation>
    </citations>

</tool>