| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/3.1.1.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/1.126.0 |
| picard_SortSam |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| picard | 3.1.1 | package |
| Additional information about this tool |
#if $sort_order == "queryname":
#set $output = "output.sam"
ln -sf '${outFile}' output.sam &&
#else:
#set $output = $outFile
#end if
_JAVA_OPTIONS=\${_JAVA_OPTIONS:-"-Xmx2048m -Xms256m -Djava.io.tmpdir=\${TMPDIR:-\${_GALAXY_JOB_TMPDIR}}"} &&
export _JAVA_OPTIONS &&
#import re
#set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
ln -sf '$inputFile' '$escaped_element_identifier' &&
picard SortSam
--INPUT '$escaped_element_identifier'
--OUTPUT '${output}'
--SORT_ORDER '${sort_order}'
--QUIET true
--VERBOSITY ERROR
--VALIDATION_STRINGENCY ${validation_stringency}
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
inputFile: picard_SortSam.bam sort_order: queryname |
name: value |
picard_SortSam.bam value |
| Test-2 |
inputFile: picard_SortSam.bam sort_order: coordinate |
name: value |
picard_SortSam.bam value |