| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/3.1.1.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.0 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/1.126.0 |
| picard_FilterSamReads |
| 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' '$escaped_element_identifier' &&
##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order
picard SortSam
--INPUT '$escaped_element_identifier'
--OUTPUT query_sorted_bam.bam
--SORT_ORDER queryname
--VALIDATION_STRINGENCY LENIENT
--QUIET true
--VERBOSITY ERROR
&&
picard FilterSamReads
--INPUT query_sorted_bam.bam
--FILTER '${filter_type.filter}'
#if ( str( $filter_type.filter ) == "includeReadList" or str( $filter_type.filter ) == "excludeReadList" ):
--READ_LIST_FILE '${filter_type.read_list_file}'
#end if
--OUTPUT '${outFile}'
--SORT_ORDER coordinate
--VALIDATION_STRINGENCY '${validation_stringency}'
--QUIET true
--VERBOSITY ERROR
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
inputFile: picard_FilterSamReads.bam filter_type|read_list_file: picard_FilterSamReads_read_list_file.tab filter_type|filter: includeReadList validation_stringency: LENIENT |
name: value |
picard_FilterSamReads.bam picard_FilterSamReads_read_list_file.tab value |
| Test-2 |
inputFile: picard_FilterSamReads.bam filter_type|read_list_file: picard_FilterSamReads_read_list_file.tab filter_type|filter: excludeReadList validation_stringency: LENIENT |
name: value |
picard_FilterSamReads.bam picard_FilterSamReads_read_list_file.tab value |