Mercurial > repos > devteam > picard
diff picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml @ 12:05087b27692a draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
| author | devteam |
|---|---|
| date | Sun, 27 Nov 2016 15:11:50 -0500 |
| parents | 3a3234d7a2e8 |
| children | 7e6fd3d0f16e |
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--- a/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml Wed Nov 11 12:23:17 2015 -0500 +++ b/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml Sun Nov 27 15:11:50 2016 -0500 @@ -4,10 +4,10 @@ <import>picard_macros.xml</import> </macros> <expand macro="requirements" /> - <command> + <command detect_errors="exit_code"><![CDATA[ @java_options@ - java -jar \$JAVA_JAR_PATH/picard.jar + picard RevertOriginalBaseQualitiesAndAddMateCigar INPUT="${inputFile}" @@ -21,7 +21,7 @@ QUIET=true VERBOSITY=ERROR - </command> + ]]></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="restore_original_qualities" type="boolean" checked="True" label="Restore original qualities from the OQ field to the QUAL field if available" help="RESTORE_ORIGINAL_QUALITIES; default=True"/> @@ -41,13 +41,10 @@ <param name="restore_original_qualities" value="True"/> <param name="max_records_to_examine" value="10000"/> <param name="validation_stringency" value="LENIENT"/> - <output name="outFile" file="picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam" ftype="bam" lines_diff="2"/> + <output name="outFile" file="picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam" ftype="bam" lines_diff="4"/> </test> </tests> - <stdio> - <exit_code range="1:" level="fatal"/> - </stdio> <help>