Repository revision
5:7474b222205d

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

Pca tool metadata
Miscellaneous
Pca
Principal Coordinate Analysis for a shared file
mothur_pca
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pca/mothur_pca/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_pca/mothur_pca/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pca/mothur_pca/1.36.1.0
mothur_pca
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 '$otu' otu.dat &&

echo 'pca(
    #if $otu.is_of_type("mothur.relabund"):
        relabund=otu.dat,
    #elif $otu.is_of_type("mothur.shared"):
        shared=otu.dat,
    #end if
    #if $label:
        label=${ str($label).replace(",","-") },
    #end if
    #if $groups:
        groups=${ str($groups).replace(",","-") },
    #end if
    metric=$metric
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    
None
False
False
Functional tests
name inputs outputs required files
Test-1 savelog: True
otu: amazon.an.shared
groups: [u'forest', u'pasture']
label: [u'0.22', u'0.55']
attributes: name
amazon.an.shared
name