Mercurial > repos > devteam > picard
view picard_AddCommentsToBam.xml @ 28:881d7645d1bf draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
author | iuc |
---|---|
date | Sat, 15 Jan 2022 12:39:30 +0000 |
parents | 2a17c789e0a5 |
children | f9242e01365a |
line wrap: on
line source
<tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>add comments to BAM dataset</description> <macros> <import>picard_macros.xml</import> <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @java_options@ @symlink_element_identifier@ picard AddCommentsToBam INPUT='$escaped_element_identifier' OUTPUT="${outFile}" #for $element in $comments: COMMENT="${element.comment}" #end for QUIET=true VERBOSITY=ERROR @TMPDIR_OPTION@ 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> <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> <expand macro="citations" /> </tool>