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comparison tools/samtools/sam_merge.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="sam_merge2" name="Merge BAM Files" version="1.1.2">
2 <description>merges BAM files together</description>
3 <requirements>
4 <requirement type="package">picard</requirement>
5 </requirements>
6 <command>
7 java -Xmx2G -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/MergeSamFiles.jar MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT O=$output1 I=$input1 I=$input2
8 #for $i in $inputs
9 I=${i.input}
10 #end for
11 2&gt; $outlog
12 </command>
13 <inputs>
14 <param name="title" label="Name for the output merged bam file" type="text" default="Merged.bam"
15 help="This name will appear in your history so use it to remember what the new file in your history contains" />
16 <param name="mergeSD" value="true" type="boolean" label="Merge all component bam file headers into the merged bam file"
17 truevalue="true" falsevalue="false" checked="yes"
18 help="Control the MERGE_SEQUENCE_DICTIONARIES flag for Picard MergeSamFiles. Default (true) correctly propagates read groups and other important metadata" />
19 <param name="input1" label="First file" type="data" format="bam" />
20 <param name="input2" label="with file" type="data" format="bam" help="Need to add more files? Use controls below." />
21 <repeat name="inputs" title="Input Files">
22 <param name="input" label="Add file" type="data" format="bam" />
23 </repeat>
24 </inputs>
25 <outputs>
26 <data format="bam" name="output1" label="${title}.bam" />
27 <data format="txt" name="outlog" label="${title}_${tool.name}.log" />
28 </outputs>
29 <tests>
30 <!-- TODO: add ability to test framework to test without at least
31 one repeat element value
32 -->
33 <test>
34 <param name="title" value="test1" />
35 <param name="mergeSD" value="true" />
36 <param name="input1" value="sam_merge_in1.bam" ftype="bam" />
37 <param name="input2" value="sam_merge_in2.bam" ftype="bam" />
38 <output name="output1" file="sam_merge_out1.bam" ftype="bam" />
39 <output name="outlog" file="sam_merge_out1.log" ftype="txt" lines_diff="10"/>
40 </test>
41 <test>
42 <param name="title" value="test2" />
43 <param name="mergeSD" value="true" />
44 <param name="input1" value="sam_merge_in1.bam" ftype="bam" />
45 <param name="input2" value="sam_merge_in2.bam" ftype="bam" />
46 <param name="input" value="sam_merge_in3.bam" ftype="bam" />
47 <output name="output1" file="sam_merge_out2.bam" ftype="bam" />
48 <output name="outlog" file="sam_merge_out2.log" ftype="txt" lines_diff="10"/>
49 </test>
50 </tests>
51 <help>
52
53 **What it does**
54
55 This tool uses the Picard_ merge command to merge any number of BAM files together into one BAM file while preserving the BAM
56 metadata such as read groups
57
58 .. _Picard: http://picard.sourceforge.net/command-line-overview.shtml#MergeSamFiles
59
60 </help>
61 </tool>