<tool id="sam_merge2" name="Merge BAM Files" version="1.2.0">
    <description>merges BAM files together</description>
    <requirements>
        <requirement type="package" version="1.56.0">picard</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <regex match="Error:" />
        <regex match="Exception:" />
    </stdio>
    <command>
<![CDATA[
        java -Xmx2G
            -jar \$JAVA_JAR_PATH/MergeSamFiles.jar
            MSD=$mergeSD
            VALIDATION_STRINGENCY=LENIENT
            O="$output1"
            TMP_DIR=$__new_file_path__
            #for $input in $inputs
                I="${input}"
            #end for
]]>
    </command>
    <inputs>
        <param name="inputs" type="data" format="bam,sam" multiple="True" label="Files to merge" />
        <param name="mergeSD" type="boolean" label="Merge all component bam file headers into the merged bam file"
            truevalue="true" falsevalue="false" checked="yes" 
            help="Control the MERGE_SEQUENCE_DICTIONARIES flag for Picard MergeSamFiles. Default (true) correctly propagates read groups and other important metadata" />
    </inputs>
    <outputs>
        <data format="bam" name="output1" />
    </outputs>
    <tests>
        <test>
            <param name="mergeSD" value="true" />
            <param name="inputs" value="sam_merge_in1.bam,sam_merge_in2.bam" ftype="bam" /> 
            <output name="output1" file="sam_merge_out1.bam" ftype="bam" />
        </test>
        <test>
            <param name="mergeSD" value="true" />
            <param name="inputs" value="sam_merge_in1.bam,sam_merge_in2.bam,sam_merge_in3.bam" ftype="bam" /> 
            <output name="output1" file="sam_merge_out2.bam" ftype="bam" />
        </test>
  </tests>
  <help>
<![CDATA[
**What it does**

This tool uses the Picard_ merge command to merge any number of BAM files together into one BAM file while preserving the BAM
metadata such as read groups.

.. _Picard: http://broadinstitute.github.io/picard/
]]>
  </help>
</tool>