| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/3.1.1.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/1.126.0 |
| picard_MergeSamFiles |
| 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 MergeSamFiles
#for $element in $inputFile:
--INPUT '${element}'
#end for
--OUTPUT '${outFile}'
--MERGE_SEQUENCE_DICTIONARIES '${merge_sequence_dictionaries}'
--ASSUME_SORTED '${assume_sorted}'
#for $element in $comments:
--COMMENT '${element.comment}'
#end for
--USE_THREADING true
--SORT_ORDER coordinate
--VALIDATION_STRINGENCY '${validation_stringency}'
--QUIET true
--VERBOSITY ERROR
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
inputFile: ['picard_MergeSamFiles_input1.bam', 'picard_MergeSamFiles_input2.bam', 'picard_MergeSamFiles_input3.bam'] merge_sequence_dictionaries: False assume_sorted: False validation_stringency: LENIENT |
name: value |
picard_MergeSamFiles_input1.bam picard_MergeSamFiles_input2.bam picard_MergeSamFiles_input3.bam value |