| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/3.1.1.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.0 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.7.1.0 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/1.136.0 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/1.126.0 |
| picard_FixMateInformation |
| 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 FixMateInformation
--INPUT '${inputFile}'
--OUTPUT '${outFile}'
--ASSUME_SORTED ${assume_sorted}
--ADD_MATE_CIGAR ${add_mate_cigar}
--SORT_ORDER coordinate
--VALIDATION_STRINGENCY '${validation_stringency}'
--QUIET true
--VERBOSITY ERROR
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
inputFile: picard_FixMateInformation.bam add_mate_cigar: True assume_sorted: False validation_stringency: LENIENT |
name: value |
picard_FixMateInformation.bam value |