Mercurial > repos > devteam > picard
annotate picard_AddCommentsToBam.xml @ 9:5eaa8a968300 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
| author | devteam |
|---|---|
| date | Fri, 09 Oct 2015 17:43:13 -0400 |
| parents | 3a3234d7a2e8 |
| children | 05087b27692a |
| rev | line source |
|---|---|
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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
diff
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> | |
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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=${validation_stringency} | |
| 19 </command> | |
| 20 | |
| 21 <inputs> | |
| 22 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" /> | |
| 23 <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments"> | |
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9
5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents:
8
diff
changeset
|
24 <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/> |
| 5 | 25 </repeat> |
| 26 | |
| 27 <expand macro="VS" /> | |
| 28 | |
| 29 </inputs> | |
| 30 | |
| 31 <outputs> | |
| 32 <data name="outFile" format="bam" label="${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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