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view picard_SortSam.xml @ 21:1181366ba593 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit cbe534af56ee782e8d1aa0fa872059d2a5e42db8"
author | iuc |
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date | Mon, 17 Feb 2020 15:23:48 +0000 |
parents | a5a13ea16d17 |
children | c943f4a04af0 |
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<tool id="picard_SortSam" name="SortSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>sort SAM/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[ #if $sort_order == "queryname": #set $output = "output.sam" ln -s '${outFile}' output.sam && #else: #set $output = $outFile #end if @java_options@ @symlink_element_identifier@ picard SortSam INPUT='$escaped_element_identifier' OUTPUT='${output}' SORT_ORDER="${sort_order}" QUIET=true VERBOSITY=ERROR @TMPDIR_OPTION@ VALIDATION_STRINGENCY=${validation_stringency} ]]></command> <inputs> <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> <param name="sort_order" type="select" display="radio" label="Sort order" help="SORT_ORDER; default=coordinate. Selecting Queryname will output SAM file, as Galaxy does not support BAM files that are not coordinate sorted."> <option value="coordinate" selected="True">Coordinate</option> <option value="queryname">Queryname</option> </param> <expand macro="VS" /> </inputs> <outputs> <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Alignment sorted in ${sort_order} order"> <change_format> <when input="sort_order" value="queryname" format="sam"/> </change_format> </data> </outputs> <tests> <!-- This test fails when setting metadata on non-coordinate sorted bam files. This should be handled better in Galaxy (info as of release 16.0). Workaroudn is to produce queryname sorted sam files. <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="4"/> </test> --> <test> <param name="inputFile" ftype="bam" value="picard_SortSam.bam" /> <param name="sort_order" value="queryname"/> <output name="outFile" file="picard_SortSam_test1.sam" ftype="sam" lines_diff="4" compare="contains"/> </test> <test> <param name="inputFile" ftype="bam" value="picard_SortSam.bam" /> <param name="sort_order" value="coordinate"/> <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="4"/> </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> <expand macro="citations" /> </tool>