Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/3.1.1.0 (this tool) |
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.1 |
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/2.18.2.0 |
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/1.56.0 |
picard_ReplaceSamHeader |
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' && ## Two lines below are due to the fact that picard likes fasta files to have extension .fa #set $fasta_file="local_fasta.fa" ln -sf '${inputFile}' '${fasta_file}' && picard ReplaceSamHeader --INPUT '$escaped_element_identifier' --HEADER '${header}' --OUTPUT '${outFile}' --QUIET true --VERBOSITY ERROR
Functional tests |
name | inputs | outputs | required files |
Test-1 |
inputFile: picard_ReplaceSamHeader.bam header: picard_ReplaceSamHeader_header.bam |
name: value |
picard_ReplaceSamHeader.bam picard_ReplaceSamHeader_header.bam value |