| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/3.1.1.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/1.126.0 |
| picard_RevertOriginalBaseQualitiesAndAddMateCigar |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| picard | 3.1.1 | package |
| Additional information about this tool |
_JAVA_OPTIONS=\${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=\${TMPDIR:-\${_GALAXY_JOB_TMPDIR}}"} &&
export _JAVA_OPTIONS &&
picard 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
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
inputFile: picard_RevertOriginalBaseQualitiesAndAddMateCigar.bam restore_original_qualities: True max_records_to_examine: 10000 validation_stringency: LENIENT |
name: value |
picard_RevertOriginalBaseQualitiesAndAddMateCigar.bam value |