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comparison picard_MergeSam.xml @ 84:bc997d1de208 draft

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author devteam
date Thu, 20 Feb 2014 18:27:42 -0500
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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&gt; /dev/null
14 ##|| echo "Error running Picard MergeSamFiles" >&amp;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>