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 |