| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/3.1.1.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/1.126.0 |
| picard_EstimateLibraryComplexity |
| 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 &&
#import re
#set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
ln -sf '$inputFile' '$escaped_element_identifier' &&
picard EstimateLibraryComplexity
--INPUT '$escaped_element_identifier'
--OUTPUT '${outFile}'
--MIN_IDENTICAL_BASES '${min_identical_bases}'
--MAX_DIFF_RATE '${max_diff_rate}'
--MIN_MEAN_QUALITY '${min_mean_quality}'
--MAX_GROUP_RATIO '${max_group_ratio}'
--READ_NAME_REGEX '${ str( $read_name_regex ) }'
--OPTICAL_DUPLICATE_PIXEL_DISTANCE '${optical_duplicate_pixel_distance}'
--VALIDATION_STRINGENCY '${validation_stringency}'
--QUIET true
--VERBOSITY ERROR
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
inputFile: picard_EstimateLibraryComplexity.bam min_identical_bases: 5 max_diff_rate: 0.03 min_mean_quality: 20 max_group_ratio: 500 read_name_regex: [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. optical_duplicate_pixel_distance: 100 validation_stringency: LENIENT |
name: value |
picard_EstimateLibraryComplexity.bam value |