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comparison picard_AddCommentsToBam.xml @ 12:05087b27692a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
author devteam
date Sun, 27 Nov 2016 15:11:50 -0500
parents 5eaa8a968300
children 7e6fd3d0f16e
comparison
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11:efc56ee1ade4 12:05087b27692a
2 <description>add comments to BAM dataset</description> 2 <description>add comments to BAM dataset</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command> 7 <command detect_errors="exit_code"><![CDATA[
8 @java_options@ 8 @java_options@
9 java -jar \$JAVA_JAR_PATH/picard.jar 9 picard
10 AddCommentsToBam 10 AddCommentsToBam
11 INPUT="${inputFile}" 11 INPUT="${inputFile}"
12 OUTPUT="${outFile}" 12 OUTPUT="${outFile}"
13 #for $element in $comments: 13 #for $element in $comments:
14 COMMENT="${element.comment}" 14 COMMENT="${element.comment}"
15 #end for 15 #end for
16 QUIET=true 16 QUIET=true
17 VERBOSITY=ERROR 17 VERBOSITY=ERROR
18 VALIDATION_STRINGENCY=${validation_stringency} 18 VALIDATION_STRINGENCY=${validation_stringency}
19 </command> 19 ]]></command>
20 20
21 <inputs> 21 <inputs>
22 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" /> 22 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
23 <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments"> 23 <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments">
24 <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/> 24 <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/>
25 </repeat> 25 </repeat>
29 </inputs> 29 </inputs>
30 30
31 <outputs> 31 <outputs>
32 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/> 32 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/>
33 </outputs> 33 </outputs>
34 34
35 <stdio> 35
36 <exit_code range="1:" level="fatal"/>
37 </stdio>
38
39 <tests> 36 <tests>
40 <test> 37 <test>
41 <param name="inputFile" value="picard_AddCommentsToBam.bam" /> 38 <param name="inputFile" value="picard_AddCommentsToBam.bam" />
42 <param name="comment" value="test1" /> 39 <param name="comment" value="test1" />
43 <param name="validation_stringency" value="LENIENT" /> 40 <param name="validation_stringency" value="LENIENT" />
55 @dataset_collections@ 52 @dataset_collections@
56 53
57 @description@ 54 @description@
58 55
59 COMMENT=String 56 COMMENT=String
60 C=String Comments to add to the BAM file This option may be specified 0 or more times. 57 C=String Comments to add to the BAM file This option may be specified 0 or more times.
61 58
62 @more_info@ 59 @more_info@
63 </help> 60 </help>
64 </tool> 61 </tool>
65 62