| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/3.1.1.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.0 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.7.1.0 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/1.136.0 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/1.126.0 |
| picard_BedToIntervalList |
| 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' &&
#set $picard_dict = "localref.dict"
#set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension
ln -sf '${reference_source.ref_file}' '${ref_fasta}' &&
#if str( $reference_source.reference_source_selector ) == "history":
picard CreateSequenceDictionary
-REFERENCE '${ref_fasta}'
-OUTPUT '${picard_dict}'
-QUIET true
-VERBOSITY ERROR
&&
#else:
#set $ref_fasta = str( $reference_source.ref_file.fields.path ) ## getting path of reference fasta file (must end with .fa)
#set $picard_dict=$ref_fasta[:-2]+"dict" ## replacing .fa with .dict
#end if
picard
BedToIntervalList
--INPUT '$escaped_element_identifier'
--OUTPUT '${outFile}'
--SEQUENCE_DICTIONARY '${picard_dict}'
--QUIET true
--VERBOSITY ERROR
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
reference_source|ref_file: picard_BedToIntervalList_ref.fa reference_source|reference_source_selector: history inputFile: picard_BedToIntervalList.bed |
name: value |
picard_BedToIntervalList_ref.fa picard_BedToIntervalList.bed value |