| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_nmds/mothur_nmds/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_nmds/mothur_nmds/1.36.1.0 |
| mothur_nmds |
| 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 '$dist' dist.dat &&
ln -s '$axes' axes.dat &&
echo 'nmds(
phylip=dist.dat
#if $axes:
,axes=axes.dat
#end if
,mindim=$mindim
#if $maxdim >= $mindim:
,maxdim=$maxdim
#end if
,iters=$iters
,maxiters=$maxiters
## Mothur can't cope with scientific notation
#set epsilon_decimal = "{:.12f}".format(float($epsilon))
,epsilon=$epsilon_decimal
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
dist: amazon.dist axes: amazon.pcoa.axes mindim: 1 maxdim: 2 iters: 10 maxiters: 500 epsilon: 1e-12 savelog: True |
name: value name: value name: value name: value |
amazon.dist amazon.pcoa.axes value |