Mercurial > repos > devteam > picard
comparison picard_AddCommentsToBam.xml @ 5:3d4f1fa26f0e draft
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author | devteam |
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date | Tue, 16 Dec 2014 19:03:21 -0500 |
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children | 3a3234d7a2e8 |
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4:ab1f60c26526 | 5:3d4f1fa26f0e |
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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> | |
67 | |
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