Mercurial > repos > devteam > picard
diff picard_SortSam.xml @ 7:08f69add4d06 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
author | devteam |
---|---|
date | Sun, 27 Nov 2016 15:11:36 -0500 |
parents | 2f3cdd537834 |
children | e417b1d6288d |
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--- a/picard_SortSam.xml Mon Nov 09 11:49:09 2015 -0500 +++ b/picard_SortSam.xml Sun Nov 27 15:11:36 2016 -0500 @@ -4,44 +4,64 @@ <import>picard_macros.xml</import> </macros> <expand macro="requirements" /> - <command> + <command detect_errors="exit_code"><![CDATA[ + #if $sort_order == "queryname": + #set $output = "output.sam" + ln -s '${outFile}' output.sam && + #else: + #set $output = $outFile + #end if @java_options@ - java -jar \$JAVA_JAR_PATH/picard.jar + picard SortSam INPUT="${inputFile}" - OUTPUT="${outFile}" + OUTPUT='${output}' SORT_ORDER="${sort_order}" QUIET=true VERBOSITY=ERROR VALIDATION_STRINGENCY=${validation_stringency} - </command> - + ]]></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"> + <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}: BAM sorted in ${sort_order} order"> + <data name="outFile" format="bam" label="${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> - - <stdio> - <exit_code range="1:" level="fatal"/> - </stdio> - + + <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="2"/> + <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 @@ -56,7 +76,7 @@ SORT_ORDER=SortOrder SO=SortOrder Sort order of output file. You can either sort by queryname or by coordinate. - + @more_info@ </help>