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view picard_MergeSamFiles.xml @ 6:961236c5ec73 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author | devteam |
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date | Mon, 09 Nov 2015 11:49:09 -0500 |
parents | 2589e6207cb4 |
children | 08f69add4d06 |
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<tool name="MergeSamFiles" id="picard_MergeSamFiles" version="@TOOL_VERSION@.0"> <description>merges multiple SAM/BAM datasets into one</description> <macros> <import>picard_macros.xml</import> </macros> <expand macro="requirements" /> <command> @java_options@ java -jar \$JAVA_JAR_PATH/picard.jar MergeSamFiles #for $element in $inputFile: INPUT="${element}" #end for OUTPUT="${outFile}" MERGE_SEQUENCE_DICTIONARIES="${merge_sequence_dictionaries}" ASSUME_SORTED="${assume_sorted}" #for $element in $comments: COMMENT="${element.comment}" #end for 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="2"/> </test> </tests> <stdio> <exit_code range="1:" level="fatal"/> </stdio> <help> **Purpose** Merges multiple SAM/BAM datasets into one. @dataset_collections@ @description@ ASSUME_SORTED=Boolean AS=Boolean If true, assume that the input files are in the same sort order as the requested output sort order, even if their headers say otherwise. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} MERGE_SEQUENCE_DICTIONARIES=Boolean MSD=Boolean Merge the sequence dictionaries Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} COMMENT=String CO=String Comment(s) to include in the merged output file's header. This option may be specified 0 or more times. @more_info@ </help> </tool>