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+ − 1 <tool id="picard_mergesam" name="Merge SAM or BAM files" version="1.106.0">
+ − 2 <!-- Documentation: http://picard.sourceforge.net/command-line-overview.shtml#MergeSamFiles
+ − 3 Merges multiple SAM/BAM files into one file.
+ − 4 -->
+ − 5 <description>merges SAM or BAM files together</description>
+ − 6 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
+ − 7 <command interpreter="bash">
+ − 8 mergesam_wrapper.sh $output1 $outformat I=$input1 I=$input2
+ − 9 #for $i in $inputs
+ − 10 I=${i.input}
+ − 11 #end for
+ − 12 MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT TMP_DIR=$__new_file_path__
+ − 13 2> /dev/null
+ − 14 ##|| echo "Error running Picard MergeSamFiles" >&2
+ − 15 </command>
+ − 16 <inputs>
+ − 17 <param name="title" label="Name for the output merged bam file" type="text" default="Merged.bam"
+ − 18 help="This name will appear in your history so use it to remember what the new file in your history contains" />
+ − 19 <param name="outformat" type="select" label="Output format" >
+ − 20 <option value="bam" selected="True">BAM</option>
+ − 21 <option value="sam">SAM</option>
+ − 22 </param>
+ − 23 <param name="mergeSD" value="true" type="boolean" label="Merge all component bam file headers into the merged bam file"
+ − 24 truevalue="true" falsevalue="false" checked="yes"
+ − 25 help="Control the MERGE_SEQUENCE_DICTIONARIES flag for Picard MergeSamFiles. Default (true) correctly propagates read groups and other important metadata" />
+ − 26 <param name="input1" label="First file" type="data" format="bam,sam" />
+ − 27 <param name="input2" label="with file" type="data" format="bam,sam" help="Need to add more files? Use controls below." />
+ − 28 <repeat name="inputs" title="Input Files">
+ − 29 <param name="input" label="Add file" type="data" format="bam,sam" />
+ − 30 </repeat>
+ − 31 </inputs>
+ − 32 <outputs>
+ − 33 <data format="bam" name="output1" label="${title}.${outformat}" >
+ − 34 <change_format>
+ − 35 <when input="outformat" value="sam" format="sam" />
+ − 36 </change_format>
+ − 37 </data>
+ − 38 </outputs>
+ − 39 <tests>
+ − 40 <test>
+ − 41 <!-- command: java -jar MergeSamFiles.jar O=mergesie.bam I=picard_output_fixmate_tiny.bam I=picard_RS_output1.bam MSD=True VALIDATION_STRINGENCY=LENIENT -->
+ − 42 <param name="title" value="test1" />
+ − 43 <param name="mergeSD" value="True" />
+ − 44 <param name="input1" value="picard_output_fixmate_tiny.bam" ftype="bam" />
+ − 45 <param name="input2" value="picard_RS_output1.bam" ftype="bam" />
+ − 46 <output name="output1" file="mergesie.bam" ftype="bam" />
+ − 47 </test>
+ − 48 </tests>
+ − 49 <help>
+ − 50
+ − 51 **What it does**
+ − 52
+ − 53 This tool uses the Picard_ merge command to merge any number of BAM files together into one BAM file while preserving the BAM
+ − 54 metadata such as read groups
+ − 55
+ − 56 .. _Picard: http://picard.sourceforge.net/command-line-overview.shtml#MergeSamFiles
+ − 57
+ − 58 </help>
+ − 59 </tool>