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view picard_MergeSam.xml @ 79:4db64daa7f5a draft
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author | devteam |
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date | Thu, 20 Feb 2014 13:31:57 -0500 |
parents | b4f78b7ad8b1 |
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<tool id="picard_mergesam" name="Merge SAM or BAM files" version="1.106.0"> <!-- Documentation: http://picard.sourceforge.net/command-line-overview.shtml#MergeSamFiles Merges multiple SAM/BAM files into one file. --> <description>merges SAM or BAM files together</description> <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements> <command interpreter="bash"> mergesam_wrapper.sh $output1 $outformat I=$input1 I=$input2 #for $i in $inputs I=${i.input} #end for MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT TMP_DIR=$__new_file_path__ 2> $outlog ##|| echo "Error running Picard MergeSamFiles" >&2 </command> <inputs> <param name="title" label="Name for the output merged bam file" type="text" default="Merged.bam" help="This name will appear in your history so use it to remember what the new file in your history contains" /> <param name="outformat" type="select" label="Output format" > <option value="bam" selected="True">BAM</option> <option value="sam">SAM</option> </param> <param name="mergeSD" value="true" type="boolean" label="Merge all component bam file headers into the merged bam file" truevalue="true" falsevalue="false" checked="yes" help="Control the MERGE_SEQUENCE_DICTIONARIES flag for Picard MergeSamFiles. Default (true) correctly propagates read groups and other important metadata" /> <param name="input1" label="First file" type="data" format="bam,sam" /> <param name="input2" label="with file" type="data" format="bam,sam" help="Need to add more files? Use controls below." /> <repeat name="inputs" title="Input Files"> <param name="input" label="Add file" type="data" format="bam,sam" /> </repeat> </inputs> <outputs> <data format="bam" name="output1" label="${title}.${outformat}" > <change_format> <when input="outformat" value="sam" format="sam" /> </change_format> </data> <data format="txt" name="outlog" label="${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>