<tool id="sam_merge2" name="Merge BAM Files" version="1.1.2">
  <description>merges BAM files together</description>
  <requirements>
    <requirement type="package" version="1.56.0">picard</requirement>
  </requirements>
  <command>
java -Xmx2G -jar \$JAVA_JAR_PATH/MergeSamFiles.jar MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT O=$output1 I=$input1 I=$input2 TMP_DIR=$__new_file_path__
      #for $i in $inputs
        I=${i.input}
      #end for 
    2&gt; $outlog
    || echo "Error running Picard MergeSamFiles" >&amp;2
  </command>
  <inputs>
    <param name="title" label="Name for the output merged bam file" type="text" default="Merged.bam"
       help="This name will appear in your history so use it to remember what the new file in your history contains" />
    <param name="mergeSD" value="true" type="boolean"  label="Merge all component bam file headers into the merged bam file"
      truevalue="true" falsevalue="false" checked="yes" 
      help="Control the MERGE_SEQUENCE_DICTIONARIES flag for Picard MergeSamFiles. Default (true) correctly propagates read groups and other important metadata" />
    <param name="input1" label="First file" type="data" format="bam,sam" />
    <param name="input2" label="with file" type="data" format="bam,sam" help="Need to add more files? Use controls below." />
    <repeat name="inputs" title="Input Files">
      <param name="input" label="Add file" type="data" format="bam,sam" />
    </repeat>
  </inputs>
  <outputs>
    <data format="bam" name="output1" label="${title}.bam" />
    <data format="txt" name="outlog" label="${title}_${tool.name}.log" />
  </outputs>
  <tests>
    <!-- TODO: add ability to test framework to test without at least 
         one repeat element value
    -->
    <test>
      <param name="title" value="test1" />
      <param name="mergeSD" value="true" />
      <param name="input1" value="sam_merge_in1.bam" ftype="bam" /> 
      <param name="input2" value="sam_merge_in2.bam" ftype="bam" />
      <output name="output1" file="sam_merge_out1.bam" ftype="bam" />
      <output name="outlog" file="sam_merge_out1.log" ftype="txt" lines_diff="11"/>
    </test>
    <test>
      <param name="title" value="test2" />
      <param name="mergeSD" value="true" />
      <param name="input1" value="sam_merge_in1.bam" ftype="bam" /> 
      <param name="input2" value="sam_merge_in2.bam" ftype="bam" />
      <param name="input" value="sam_merge_in3.bam" ftype="bam" />
      <output name="output1" file="sam_merge_out2.bam" ftype="bam" />
      <output name="outlog" file="sam_merge_out2.log" ftype="txt" lines_diff="11"/>
    </test>
  </tests>
  <help>

**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://picard.sourceforge.net/command-line-overview.shtml#MergeSamFiles

  </help>
</tool>