| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/3.1.1.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/1.126.0 |
| picard_AddCommentsToBam |
| 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 &&
## linking does not work, picard complains about not writable file. Hopefully this can be removed in future version.
##
#import re
#set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
ln -sf '$inputFile' '$escaped_element_identifier' &&
#import re
#set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
cp '$inputFile' '$escaped_element_identifier' &&
picard
AddCommentsToBam
--INPUT '$escaped_element_identifier'
--OUTPUT '${outFile}'
#for $element in $comments:
--COMMENT '${element.comment}'
#end for
--QUIET true
--VERBOSITY ERROR
--VALIDATION_STRINGENCY ${validation_stringency}
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
inputFile: picard_AddCommentsToBam.bam comments_0|comment: test1 validation_stringency: LENIENT |
name: value |
picard_AddCommentsToBam.bam value |