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comparison picard_AddCommentsToBam.xml @ 5:3d4f1fa26f0e draft

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author devteam
date Tue, 16 Dec 2014 19:03:21 -0500
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4:ab1f60c26526 5:3d4f1fa26f0e
1 <tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="1.126.0">
2 <description>add comments to BAM dataset</description>
3 <requirements><requirement type="package" version="1.126.0">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/picard.jar
12 AddCommentsToBam
13 INPUT="${inputFile}"
14 OUTPUT="${outFile}"
15 #for $element in $comments:
16 COMMENT="${element.comment}"
17 #end for
18 QUIET=true
19 VERBOSITY=ERROR
20 VALIDATION_STRINGENCY=${validation_stringency}
21 </command>
22
23 <inputs>
24 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
25 <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments">
26 <param name="comment" type="text" size="50" label="Add this comment to BAM dataset" help="COMMENT"/>
27 </repeat>
28
29 <expand macro="VS" />
30
31 </inputs>
32
33 <outputs>
34 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/>
35 </outputs>
36
37 <stdio>
38 <exit_code range="1:" level="fatal"/>
39 </stdio>
40
41 <tests>
42 <test>
43 <param name="inputFile" value="picard_AddCommentsToBam.bam" />
44 <param name="comment" value="test1" />
45 <param name="validation_stringency" value="LENIENT" />
46 <output name="outFile" file="picard_AddCommentsToBam_test1.bam" ftype="bam" />
47 </test>
48 </tests>
49 <help>
50
51 .. class:: infomark
52
53 **Purpose**
54
55 Adds one or more comments (@CO) to the header of a specified BAM dataset.
56
57 @dataset_collections@
58
59 @description@
60
61 COMMENT=String
62 C=String Comments to add to the BAM file This option may be specified 0 or more times.
63
64 @more_info@
65 </help>
66 </tool>
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