Mercurial > repos > devteam > picard
view picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml @ 6:961236c5ec73 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author | devteam |
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date | Mon, 09 Nov 2015 11:49:09 -0500 |
parents | 52fdfc45590a |
children | 08f69add4d06 |
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<tool name="RevertOriginalBaseQualitiesAndAddMateCigar" id="picard_RevertOriginalBaseQualitiesAndAddMateCigar" version="@TOOL_VERSION@.0"> <description>revert the original base qualities and add the mate cigar tag</description> <macros> <import>picard_macros.xml</import> </macros> <expand macro="requirements" /> <command> @java_options@ java -jar \$JAVA_JAR_PATH/picard.jar RevertOriginalBaseQualitiesAndAddMateCigar INPUT="${inputFile}" OUTPUT="${outFile}" RESTORE_ORIGINAL_QUALITIES="${restore_original_qualities}" MAX_RECORDS_TO_EXAMINE="${max_records_to_examine}" SORT_ORDER=coordinate VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR </command> <inputs> <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> <param name="restore_original_qualities" type="boolean" checked="True" label="Restore original qualities from the OQ field to the QUAL field if available" help="RESTORE_ORIGINAL_QUALITIES; default=True"/> <param name="max_records_to_examine" type="integer" value="10000" min="0" label="The maximum number of records to examine to determine if we can exit early and not output, given that there are a no original base qualities (if we are to restore) and mate cigars exist. Set to 0 to never skip the dataset" help="MAX_RECORDS_TO_EXAMINE; default=10,000"/> <expand macro="VS" /> </inputs> <outputs> <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Reverted BAM dataset"/> </outputs> <tests> <test> <param name="inputFile" value="picard_RevertOriginalBaseQualitiesAndAddMateCigar.bam" ftype="bam"/> <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"/> </test> </tests> <stdio> <exit_code range="1:" level="fatal"/> </stdio> <help> **Purpose** Reverts the original base qualities and adds the mate cigar tag to SAM or BAMs. @dataset_collections@ @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 cigars exist. Set to 0 to never skip the file. Default value: 10000. @more_info@ </help> </tool>