Repository revision
9:ffdcb7942343

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

Cooccurrence tool metadata
Miscellaneous
Cooccurrence
tests whether presence-absence patterns differ from chance
mothur_cooccurrence
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cooccurrence/mothur_cooccurrence/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_cooccurrence/mothur_cooccurrence/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cooccurrence/mothur_cooccurrence/1.36.1.0
mothur_cooccurrence
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 'cooccurrence(
    shared=otu.dat,
    metric=$metric,
    matrixmodel=$matrixmodel,
    iters=$iters
    #if $label:
        ,label=${ str($label).replace(",","-") }
    #end if
    #if $groups:
        ,groups=${ str($groups).replace(",","-") }
    #end if
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    
None
False
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
metric: vratio
groups: ['forest', 'pasture']
label: ['0.05', '0.22', '0.41']
savelog: True
name: value
name: value
amazon.an.shared
value