Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/mothur_sffinfo/mothur_sffinfo/1.39.5.0 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/mothur_sffinfo/mothur_sffinfo/1.36.1.0 |
mothur_sffinfo |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
mothur | 1.39.5 | package |
Additional information about this tool |
set -o pipefail; export TERM=vt100; ## create symlinks to input datasets ln -s '$sff' sff.dat && ln -s '$accnos' accnos.dat && #if $oligo.add == "yes": ln -s '$oligo.oligos' oligo.oligos.dat && #end if echo 'sffinfo( sff=sff.dat, fasta=$fasta, qfile=$qfile, $sfftxt flow=$flow, trim=$trim #if $accnos: ,accnos=accnos.dat #end if #if $oligo.add == "yes": ,oligos=oligo.oligos.dat ,bdiffs=$oligo.bdiffs ,pdiffs=$oligo.pdiffs ,tdiffs=$oligo.tdiffs ,ldiffs=$oligo.ldiffs ,sdiffs=$oligo.sdiffs #end if )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log
Functional tests |
name | inputs | outputs | required files |
Test-1 |
sff: Fasting_Example1.sff sfftxt: True savelog: True |
name: value name: value name: value name: value name: value |
Fasting_Example1.sff value |
Test-2 |
sff: Fasting_Example1.sff oligo|oligos: GQY1XT001.oligos oligo|add: yes savelog: True |
name: value name: value name: value name: value name: value |
Fasting_Example1.sff GQY1XT001.oligos value |