Mercurial > repos > devteam > picard
annotate picard_AddCommentsToBam.xml @ 11:efc56ee1ade4 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
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date | Wed, 11 Nov 2015 12:23:17 -0500 |
parents | 5eaa8a968300 |
children | 05087b27692a |
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3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
5
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changeset
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1 <tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="@TOOL_VERSION@.0"> |
5 | 2 <description>add comments to BAM dataset</description> |
3 <macros> | |
4 <import>picard_macros.xml</import> | |
5 </macros> | |
8
3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
5
diff
changeset
|
6 <expand macro="requirements" /> |
5 | 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=${validation_stringency} | |
19 </command> | |
20 | |
21 <inputs> | |
22 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" /> | |
23 <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments"> | |
9
5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents:
8
diff
changeset
|
24 <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/> |
5 | 25 </repeat> |
26 | |
27 <expand macro="VS" /> | |
28 | |
29 </inputs> | |
30 | |
31 <outputs> | |
32 <data name="outFile" format="bam" label="${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> | |
65 | |
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