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comparison picard_AddCommentsToBam.xml @ 3:52fdfc45590a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Thu, 16 Jul 2015 15:32:31 -0400
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children 2589e6207cb4
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2:93ace7e49295 3:52fdfc45590a
1 <tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="@TOOL_VERSION@.0">
2 <description>add comments to BAM dataset</description>
3 <macros>
4 <import>picard_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>
8 @java_options@
9 java -jar \$JAVA_JAR_PATH/picard.jar
10 AddCommentsToBam
11 INPUT="${inputFile}"
12 OUTPUT="${outFile}"
13 #for $element in $comments:
14 COMMENT="${element.comment}"
15 #end for
16 QUIET=true
17 VERBOSITY=ERROR
18 VALIDATION_STRINGENCY=${validation_stringency}
19 </command>
20
21 <inputs>
22 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
23 <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments">
24 <param name="comment" type="text" size="50" label="Add this comment to BAM dataset" help="COMMENT"/>
25 </repeat>
26
27 <expand macro="VS" />
28
29 </inputs>
30
31 <outputs>
32 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/>
33 </outputs>
34
35 <stdio>
36 <exit_code range="1:" level="fatal"/>
37 </stdio>
38
39 <tests>
40 <test>
41 <param name="inputFile" value="picard_AddCommentsToBam.bam" />
42 <param name="comment" value="test1" />
43 <param name="validation_stringency" value="LENIENT" />
44 <output name="outFile" file="picard_AddCommentsToBam_test1.bam" ftype="bam" />
45 </test>
46 </tests>
47 <help>
48
49 .. class:: infomark
50
51 **Purpose**
52
53 Adds one or more comments (@CO) to the header of a specified BAM dataset.
54
55 @dataset_collections@
56
57 @description@
58
59 COMMENT=String
60 C=String Comments to add to the BAM file This option may be specified 0 or more times.
61
62 @more_info@
63 </help>
64 </tool>
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