Mercurial > repos > devteam > picard
diff picard_FilterSamReads.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 | 52fdfc45590a |
children | e417b1d6288d |
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--- a/picard_FilterSamReads.xml Mon Nov 09 11:49:09 2015 -0500 +++ b/picard_FilterSamReads.xml Sun Nov 27 15:11:36 2016 -0500 @@ -4,12 +4,12 @@ <import>picard_macros.xml</import> </macros> <expand macro="requirements" /> - <command> + <command detect_errors="exit_code"><![CDATA[ @java_options@ ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order - java -jar \$JAVA_JAR_PATH/picard.jar + picard SortSam INPUT="${inputFile}" OUTPUT=query_sorted_bam.bam @@ -18,9 +18,9 @@ QUIET=true VERBOSITY=ERROR - && + && - java -jar \$JAVA_JAR_PATH/picard.jar + picard FilterSamReads INPUT=query_sorted_bam.bam FILTER="${filter_type.filter}" @@ -35,7 +35,7 @@ QUIET=true VERBOSITY=ERROR - </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"/> <conditional name="filter_type"> @@ -69,20 +69,17 @@ <param name="filter" value="includeReadList"/> <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/> <param name="validation_stringency" value="LENIENT"/> - <output name="outFile" file="picard_FilterSamReads_include_reads_test1.bam" ftype="bam" lines_diff="2"/> + <output name="outFile" file="picard_FilterSamReads_include_reads_test1.bam" ftype="bam" lines_diff="4"/> </test> <test> <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/> <param name="filter" value="excludeReadList"/> <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/> <param name="validation_stringency" value="LENIENT"/> - <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="2"/> + <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="4"/> </test> </tests> - <stdio> - <exit_code range="1:" level="fatal"/> - </stdio> <help>