Repository revision
5:98f1cc2bc428

Repository 'mothur_nmds'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/mothur_nmds

Nmds tool metadata
Miscellaneous
Nmds
generate non-metric multidimensional scaling data
mothur_nmds
toolshed.g2.bx.psu.edu/repos/iuc/mothur_nmds/mothur_nmds/1.39.5.0
1.39.5.0
mothur "#help()" | sed '7q;d' | cut -d" " -f2
True
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;

## 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
    
None
False
False
Functional tests
name inputs outputs required files
Test-1 axes: amazon.pcoa.axes
dist: amazon.dist
iters: 10
epsilon: 1e-12
maxiters: 500
savelog: True
mindim: 1
maxdim: 2
attributes: name
attributes: name
attributes: name
attributes: name
amazon.dist
amazon.pcoa.axes
name