| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_shared/mothur_rarefaction_shared/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_shared/mothur_rarefaction_shared/1.36.1.0 |
| mothur_rarefaction_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 &&
#if $designc.usedesign == "yes":
ln -s '$designc.design' designc.design.dat &&
#end if
echo 'rarefaction.shared(
shared=otu.dat,
#if $label:
label=${ str($label).replace(",","-") },
#end if
#if $groups
groups=${ str($groups).replace(",","-") },
#end if
#if $designc.usedesign == "yes":
design=designc.design.dat,
#if $designc.sets:
sets=${ str($designc.sets).replace(",","-") },
#end if
#end if
#if $subsample.usess == "yes":
#if $subsample.subsamplesize:
subsample=$subsample.subsamplesize,
#else
subsample=T,
#end if
#if $subsample.subsampleiters:
subsampleiters=$subsample.subsampleiters,
#end if
#end if
calc=${ str($calc).replace(",","-") },
iters=$iters
$jumble
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
otu: amazon.an.shared savelog: True |
name: value name: value |
amazon.an.shared value |
| Test-2 |
otu: amazon.an.shared label: ['0.22', '0.55'] groups: ['forest', 'pasture'] calc: ['sharedobserved', 'sharednseqs'] savelog: True |
name: value name: value name: value |
amazon.an.shared value |
| Test-3 |
otu: amazon.an.shared designc|design: toymothur.design2 designc|sets: ['tardis', 'dalek'] designc|usedesign: yes savelog: True |
name: value name: value |
amazon.an.shared toymothur.design2 value |