Mercurial > repos > devteam > picard
view picard_SortSam.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 | 2f3cdd537834 |
children | 08f69add4d06 |
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<tool id="picard_SortSam" name="SortSam" version="@TOOL_VERSION@.1"> <description>sort SAM/BAM dataset</description> <macros> <import>picard_macros.xml</import> </macros> <expand macro="requirements" /> <command> @java_options@ java -jar \$JAVA_JAR_PATH/picard.jar SortSam INPUT="${inputFile}" OUTPUT="${outFile}" SORT_ORDER="${sort_order}" QUIET=true VERBOSITY=ERROR VALIDATION_STRINGENCY=${validation_stringency} </command> <inputs> <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> <param name="sort_order" type="select" display="radio" label="Sort order" help="SORT_ORDER; default=coordinate"> <option value="coordinate" selected="True">Coordinate</option> <option value="queryname">Queryname</option> </param> <expand macro="VS" /> </inputs> <outputs> <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM sorted in ${sort_order} order"> </data> </outputs> <stdio> <exit_code range="1:" level="fatal"/> </stdio> <tests> <test> <param name="inputFile" ftype="bam" value="picard_SortSam.bam" /> <param name="sort_order" value="queryname"/> <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="2"/> </test> </tests> <help> .. class:: infomark **Purpose** Sorts the input SAM or BAM. @dataset_collections@ @description@ SORT_ORDER=SortOrder SO=SortOrder Sort order of output file. You can either sort by queryname or by coordinate. @more_info@ </help> </tool>