Mercurial > repos > devteam > picard1106
diff picard_MergeSam.xml @ 84:bc997d1de208 draft
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author | devteam |
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date | Thu, 20 Feb 2014 18:27:42 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_MergeSam.xml Thu Feb 20 18:27:42 2014 -0500 @@ -0,0 +1,59 @@ +<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> /dev/null + ##|| 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> + </outputs> + <tests> + <test> + <!-- command: java -jar MergeSamFiles.jar O=mergesie.bam I=picard_output_fixmate_tiny.bam I=picard_RS_output1.bam MSD=True VALIDATION_STRINGENCY=LENIENT --> + <param name="title" value="test1" /> + <param name="mergeSD" value="True" /> + <param name="input1" value="picard_output_fixmate_tiny.bam" ftype="bam" /> + <param name="input2" value="picard_RS_output1.bam" ftype="bam" /> + <output name="output1" file="mergesie.bam" ftype="bam" /> + </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>