Repository revision
9:528f950d1044

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

Cluster tool metadata
Miscellaneous
Cluster
Assign sequences to OTUs (Operational Taxonomic Unit)
mothur_cluster
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/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_cluster/mothur_cluster/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.36.1.0
mothur_cluster
Requirements (dependencies defined in the <requirements> tag set)
name version type
mothur 1.39.5 package
vsearch 2.6.0 package
Additional information about this tool
set -o pipefail; export TERM=vt100; 

## create symlinks to input datasets
ln -s '$matrix.dist' matrix.dist.dat &&
ln -s '$matrix.name' matrix.name.dat &&
ln -s '$count' count.dat &&

echo 'cluster(
    #if $matrix.format == "phylip":
        phylip=matrix.dist.dat,
    #else
        column=matrix.dist.dat,
    #end if
    #if $matrix.name:
        name=matrix.name.dat,
    #end if
    #if $count:
        count=count.dat,
    #end if
    #if float($cutoff) > 0.0:
        cutoff=$cutoff,
    #end if
    #if $select_method.method =="opti":
        metric=$select_method.metric,
        initialize=$select_method.initialize,
        delta=$select_method.delta,
        iters=$select_method.iters,
    #end if
    precision=$precision,
    sim=$sim,
    method=$select_method.method
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    
None
False
Functional tests
name inputs outputs required files
Test-1 matrix|dist: amazon.dist
matrix|format: phylip
savelog: True
name: value
name: value
name: value
name: value
amazon.dist
value
Test-2 matrix|dist: amazon.pair.dist
matrix|name: amazon.names
matrix|format: column
savelog: True
name: value
name: value
name: value
name: value
amazon.pair.dist
amazon.names
value
Test-3 matrix|dist: amazon.pair.dist
matrix|name: amazon.names
matrix|format: column
savelog: True
name: value
name: value
name: value
name: value
amazon.pair.dist
amazon.names
value