Mercurial > repos > devteam > picard
diff picard_AddCommentsToBam.xml @ 33:3f254c5ced1d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
| author | iuc |
|---|---|
| date | Sun, 03 Mar 2024 16:06:11 +0000 |
| parents | f9242e01365a |
| children |
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--- a/picard_AddCommentsToBam.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_AddCommentsToBam.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,49 +1,48 @@ -<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[ +<tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@"> + <description>add comments to BAM dataset</description> + <macros> + <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ @java_options@ - @symlink_element_identifier@ + ## linking does not work, picard complains about not writable file. Hopefully this can be removed in future version. + ##@symlink_element_identifier@ + #import re + #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier)) + cp '$inputFile' '$escaped_element_identifier' && + picard AddCommentsToBam - INPUT='$escaped_element_identifier' - OUTPUT="${outFile}" + --INPUT '$escaped_element_identifier' + --OUTPUT '${outFile}' #for $element in $comments: - COMMENT="${element.comment}" + --COMMENT '${element.comment}' #end for - QUIET=true - VERBOSITY=ERROR - VALIDATION_STRINGENCY=${validation_stringency} + --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 ${on_string}: BAM with comments"/> - </outputs> - - - <tests> - <test> - <param name="inputFile" value="picard_AddCommentsToBam.bam" /> - <param name="comment" value="test1" /> - <param name="validation_stringency" value="LENIENT" /> - <output name="outFile" file="picard_AddCommentsToBam_test1.bam" ftype="bam" /> - </test> - </tests> - <help> + <inputs> + <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> + <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments"> + <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/> + </repeat> + <expand macro="VS"/> + </inputs> + <outputs> + <data name="outFile" format="bam" label="${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 @@ -60,5 +59,5 @@ @more_info@ </help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>