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 |