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comparison picard_AddCommentsToBam.xml @ 0:4419e9980172 draft

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author devteam
date Thu, 23 Oct 2014 12:03:34 -0400
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1 <tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="1.122.0">
2 <description>add comments to BAM dataset</description>
3 <requirements><requirement type="package" version="1.122.0">picard</requirement></requirements>
4
5 <macros>
6 <import>picard_macros.xml</import>
7 </macros>
8
9 <command>
10 @java_options@
11 java -jar \$JAVA_JAR_PATH/AddCommentsToBam.jar
12 INPUT="${inputFile}"
13 OUTPUT="${outFile}"
14 #for $element in $comments:
15 COMMENT="${element.comment}"
16 #end for
17 QUIET=true
18 VERBOSITY=ERROR
19 VALIDATION_STRINGENCY=${validation_stringency}
20 </command>
21
22 <inputs>
23 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
24 <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments">
25 <param name="comment" type="text" size="50" label="Add this comment to BAM dataset" help="COMMENT"/>
26 </repeat>
27
28 <expand macro="VS" />
29
30 </inputs>
31
32 <outputs>
33 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/>
34 </outputs>
35
36 <stdio>
37 <exit_code range="1:" level="fatal"/>
38 </stdio>
39
40 <tests>
41 <test>
42 <param name="inputFile" value="picard_AddCommentsToBam.bam" />
43 <param name="comment" value="test1" />
44 <param name="validation_stringency" value="LENIENT" />
45 <output name="outFile" file="picard_AddCommentsToBam_test1.bam" ftype="bam" />
46 </test>
47 </tests>
48 <help>
49
50 .. class:: infomark
51
52 **Purpose**
53
54 Adds one or more comments (@CO) to the header of a specified BAM dataset.
55
56 @dataset_collections@
57
58 @description@
59
60 COMMENT=String
61 C=String Comments to add to the BAM file This option may be specified 0 or more times.
62
63 @more_info@
64 </help>
65 </tool>
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