Mercurial > repos > devteam > picard
diff picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml @ 13:7e6fd3d0f16e draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author | devteam |
---|---|
date | Tue, 06 Dec 2016 10:04:41 -0500 |
parents | 05087b27692a |
children | 5053a18d9bc8 |
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--- a/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml Sun Nov 27 15:11:50 2016 -0500 +++ b/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml Tue Dec 06 10:04:41 2016 -0500 @@ -6,21 +6,20 @@ <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @java_options@ - picard RevertOriginalBaseQualitiesAndAddMateCigar - - INPUT="${inputFile}" + + INPUT='$inputFile' OUTPUT="${outFile}" - + RESTORE_ORIGINAL_QUALITIES="${restore_original_qualities}" MAX_RECORDS_TO_EXAMINE="${max_records_to_examine}" - + SORT_ORDER=coordinate VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - + ]]></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"/> @@ -28,13 +27,13 @@ <param name="max_records_to_examine" type="integer" value="10000" min="0" label="The maximum number of records to examine to determine if we can exit early and not output, given that there are a no original base qualities (if we are to restore) and mate cigars exist. Set to 0 to never skip the dataset" help="MAX_RECORDS_TO_EXAMINE; default=10,000"/> <expand macro="VS" /> - - </inputs> - + + </inputs> + <outputs> <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Reverted BAM dataset"/> </outputs> - + <tests> <test> <param name="inputFile" value="picard_RevertOriginalBaseQualitiesAndAddMateCigar.bam" ftype="bam"/> @@ -44,8 +43,8 @@ <output name="outFile" file="picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam" ftype="bam" lines_diff="4"/> </test> </tests> - - + + <help> **Purpose** @@ -57,11 +56,11 @@ @description@ RESTORE_ORIGINAL_QUALITIES=Boolean - OQ=Boolean True to restore original qualities from the OQ field to the QUAL field if available. - Default value: true. Possible values: {true, false} - - MAX_RECORDS_TO_EXAMINE=IntegerThe maximum number of records to examine to determine if we can exit early and not - output, given that there are a no original base qualities (if we are to restore) and mate + OQ=Boolean True to restore original qualities from the OQ field to the QUAL field if available. + Default value: true. Possible values: {true, false} + + MAX_RECORDS_TO_EXAMINE=IntegerThe maximum number of records to examine to determine if we can exit early and not + output, given that there are a no original base qualities (if we are to restore) and mate cigars exist. Set to 0 to never skip the file. Default value: 10000. @more_info@