| 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 |