| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/3.1.1.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.0 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.7.1.0 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/1.136.0 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/1.126.0 |
| picard_NormalizeFasta |
| 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 &&
## Two lines below are due to the fact that picard likes fasta files to have extension .fa
#import re
#set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
ln -sf '$inputFile' '$escaped_element_identifier'.fa &&
picard NormalizeFasta
--INPUT '$escaped_element_identifier'.fa
--OUTPUT '${outFile}'
--LINE_LENGTH '${line_length}'
--TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE '${truncate_sequence_names_at_whitespaces}'
--QUIET true
--VERBOSITY ERROR
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
inputFile: picard_NormalizeFasta_ref.fa line_length: 40 truncate_sequence_names_at_whitespaces: False |
name: value |
picard_NormalizeFasta_ref.fa value |