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comparison sam_merge.xml @ 0:a7a49d31c5cf draft

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author devteam
date Mon, 26 Aug 2013 14:20:22 -0400
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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" version="1.56.0">picard</requirement>
5 </requirements>
6 <command>
7 java -Xmx2G -jar \$JAVA_JAR_PATH/MergeSamFiles.jar MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT O=$output1 I=$input1 I=$input2 TMP_DIR=$__new_file_path__
8 #for $i in $inputs
9 I=${i.input}
10 #end for
11 2&gt; $outlog
12 || echo "Error running Picard MergeSamFiles" >&amp;2
13 </command>
14 <inputs>
15 <param name="title" label="Name for the output merged bam file" type="text" default="Merged.bam"
16 help="This name will appear in your history so use it to remember what the new file in your history contains" />
17 <param name="mergeSD" value="true" type="boolean" label="Merge all component bam file headers into the merged bam file"
18 truevalue="true" falsevalue="false" checked="yes"
19 help="Control the MERGE_SEQUENCE_DICTIONARIES flag for Picard MergeSamFiles. Default (true) correctly propagates read groups and other important metadata" />
20 <param name="input1" label="First file" type="data" format="bam,sam" />
21 <param name="input2" label="with file" type="data" format="bam,sam" help="Need to add more files? Use controls below." />
22 <repeat name="inputs" title="Input Files">
23 <param name="input" label="Add file" type="data" format="bam,sam" />
24 </repeat>
25 </inputs>
26 <outputs>
27 <data format="bam" name="output1" label="${title}.bam" />
28 <data format="txt" name="outlog" label="${title}_${tool.name}.log" />
29 </outputs>
30 <tests>
31 <!-- TODO: add ability to test framework to test without at least
32 one repeat element value
33 -->
34 <test>
35 <param name="title" value="test1" />
36 <param name="mergeSD" value="true" />
37 <param name="input1" value="sam_merge_in1.bam" ftype="bam" />
38 <param name="input2" value="sam_merge_in2.bam" ftype="bam" />
39 <output name="output1" file="sam_merge_out1.bam" ftype="bam" />
40 <output name="outlog" file="sam_merge_out1.log" ftype="txt" lines_diff="11"/>
41 </test>
42 <test>
43 <param name="title" value="test2" />
44 <param name="mergeSD" value="true" />
45 <param name="input1" value="sam_merge_in1.bam" ftype="bam" />
46 <param name="input2" value="sam_merge_in2.bam" ftype="bam" />
47 <param name="input" value="sam_merge_in3.bam" ftype="bam" />
48 <output name="output1" file="sam_merge_out2.bam" ftype="bam" />
49 <output name="outlog" file="sam_merge_out2.log" ftype="txt" lines_diff="11"/>
50 </test>
51 </tests>
52 <help>
53
54 **What it does**
55
56 This tool uses the Picard_ merge command to merge any number of BAM files together into one BAM file while preserving the BAM
57 metadata such as read groups
58
59 .. _Picard: http://picard.sourceforge.net/command-line-overview.shtml#MergeSamFiles
60
61 </help>
62 </tool>