Mercurial > repos > devteam > picard
view picard_AddCommentsToBam.xml @ 5:2f3cdd537834 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 6e148b31fed1b322ce720804d8525088ec6d43f9
author | devteam |
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date | Thu, 29 Oct 2015 22:23:28 -0400 |
parents | 2589e6207cb4 |
children | 08f69add4d06 |
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<tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="@TOOL_VERSION@.0"> <description>add comments to BAM dataset</description> <macros> <import>picard_macros.xml</import> </macros> <expand macro="requirements" /> <command> @java_options@ java -jar \$JAVA_JAR_PATH/picard.jar AddCommentsToBam INPUT="${inputFile}" OUTPUT="${outFile}" #for $element in $comments: COMMENT="${element.comment}" #end for QUIET=true VERBOSITY=ERROR VALIDATION_STRINGENCY=${validation_stringency} </command> <inputs> <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" /> <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments"> <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/> </repeat> <expand macro="VS" /> </inputs> <outputs> <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/> </outputs> <stdio> <exit_code range="1:" level="fatal"/> </stdio> <tests> <test> <param name="inputFile" value="picard_AddCommentsToBam.bam" /> <param name="comment" value="test1" /> <param name="validation_stringency" value="LENIENT" /> <output name="outFile" file="picard_AddCommentsToBam_test1.bam" ftype="bam" /> </test> </tests> <help> .. class:: infomark **Purpose** Adds one or more comments (@CO) to the header of a specified BAM dataset. @dataset_collections@ @description@ COMMENT=String C=String Comments to add to the BAM file This option may be specified 0 or more times. @more_info@ </help> </tool>