| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/3.1.1.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.0 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.7.1.0 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/1.136.0 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/1.126.0 |
| picard_RevertSam |
| 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 RevertSam
--INPUT '$inputFile'
--OUTPUT '${outFile}'
--RESTORE_ORIGINAL_QUALITIES '${restore_original_qualities}'
--REMOVE_DUPLICATE_INFORMATION '${remove_duplicate_information}'
--REMOVE_ALIGNMENT_INFORMATION '${remove_alignment_information}'
#for $attribute_to_clear in $attributes_to_clear:
--ATTRIBUTE_TO_CLEAR '${attribute_to_clear.attribute}'
#end for
--SANITIZE '${sanitize}'
--MAX_DISCARD_FRACTION '${max_discard_fraction}'
--SAMPLE_ALIAS '${sample_alias}'
--LIBRARY_NAME '${library_name}'
--SORT_ORDER '${sort_order}'
--VALIDATION_STRINGENCY '${validation_stringency}'
--QUIET true
--VERBOSITY ERROR
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
inputFile: picard_RevertSam.bam restore_original_qualities: True remove_duplicate_information: True remove_alignment_information: True attributes_to_clear_0|attribute: XM sanitize: False max_discard_fraction: 0.01 sample_alias: null library_name: null sort_order: coordinate validation_stringency: LENIENT |
name: value |
picard_RevertSam.bam value |