| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_shared/mothur_filter_shared/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_shared/mothur_filter_shared/1.36.1.0 |
| mothur_filter_shared |
| 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 '$otu' otu.dat &&
echo 'filter.shared(
shared=otu.dat,
#if $label:
label=${ str($label).replace(",","-") },
#end if
#if $label:
groups=${ str($groups).replace(",","-") },
#end if
minabund=$minabund,
minpercent=$minpercent,
rarepercent=$rarepercent,
keepties=$keepties,
minnumsamples=$minnumsamples,
minpercentsamples=$minpercentsamples,
mintotal=$mintotal,
makerare=$makerare
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
otu: esophagus.fn.shared savelog: True |
name: value |
esophagus.fn.shared value |
| Test-2 |
otu: amazon.an.shared label: ['0.05', '0.29', '0.33'] groups: ['forest', 'pasture'] minabund: 1 savelog: True |
name: value |
amazon.an.shared value |