Mercurial > repos > devteam > picard
diff picard_MergeSamFiles.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_MergeSamFiles.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_MergeSamFiles.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,63 +1,55 @@ -<tool name="MergeSamFiles" id="picard_MergeSamFiles" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> - <description>merges multiple SAM/BAM datasets into one</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="MergeSamFiles" id="picard_MergeSamFiles" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@"> + <description>merges multiple SAM/BAM datasets into one</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@ - picard - MergeSamFiles + picard MergeSamFiles #for $element in $inputFile: - INPUT="${element}" + --INPUT '${element}' #end for - OUTPUT="${outFile}" - MERGE_SEQUENCE_DICTIONARIES="${merge_sequence_dictionaries}" + --OUTPUT '${outFile}' + --MERGE_SEQUENCE_DICTIONARIES '${merge_sequence_dictionaries}' - ASSUME_SORTED="${assume_sorted}" + --ASSUME_SORTED '${assume_sorted}' #for $element in $comments: - COMMENT="${element.comment}" + --COMMENT '${element.comment}' #end for - USE_THREADING=true - SORT_ORDER=coordinate - VALIDATION_STRINGENCY="${validation_stringency}" - QUIET=true - VERBOSITY=ERROR + --USE_THREADING true + --SORT_ORDER coordinate + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR ]]></command> - <inputs> - <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> - <param name="merge_sequence_dictionaries" type="boolean" label="Merge the sequence dictionaries of the datasets being merged" help="MERGE_SEQUENCE_DICTIONARIES; default=False"/> - <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" help="ASSUME_SORTED; default=False"/> - - <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments"> - <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/> - </repeat> - - <expand macro="VS" /> - - </inputs> - - <outputs> - <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Merged BAM dataset"/> - </outputs> - - <tests> - <test> - <param name="inputFile" value="picard_MergeSamFiles_input1.bam,picard_MergeSamFiles_input2.bam,picard_MergeSamFiles_input3.bam" ftype="bam"/> - <param name="assume_sorted" value="False"/> - <param name="merge_sequence_dictionaries" value="False"/> - <param name="validation_stringency" value="LENIENT"/> - <output name="outFile" file="picard_MergeSamFiles_test1.bam" ftype="bam" lines_diff="4"/> - </test> - </tests> - - - <help> + <inputs> + <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> + <param name="merge_sequence_dictionaries" type="boolean" label="Merge the sequence dictionaries of the datasets being merged" help="MERGE_SEQUENCE_DICTIONARIES; default=False"/> + <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" help="ASSUME_SORTED; default=False"/> + <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments"> + <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/> + </repeat> + <expand macro="VS"/> + </inputs> + <outputs> + <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Merged BAM dataset"/> + </outputs> + <tests> + <test> + <param name="inputFile" value="picard_MergeSamFiles_input1.bam,picard_MergeSamFiles_input2.bam,picard_MergeSamFiles_input3.bam" ftype="bam"/> + <param name="assume_sorted" value="False"/> + <param name="merge_sequence_dictionaries" value="False"/> + <param name="validation_stringency" value="LENIENT"/> + <output name="outFile" file="picard_MergeSamFiles_test1.bam" ftype="bam" lines_diff="4"/> + </test> + </tests> + <help> **Purpose** @@ -84,5 +76,5 @@ @more_info@ </help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>