Repository revision
10:aff64115d95f

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

Parsimony tool metadata
Miscellaneous
Parsimony
Describes whether two or more communities have the same structure
mothur_parsimony
toolshed.g2.bx.psu.edu/repos/iuc/mothur_parsimony/mothur_parsimony/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_parsimony/mothur_parsimony/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_parsimony/mothur_parsimony/1.36.1.0
mothur_parsimony
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 '$tree' tree.dat &&
ln -s '$group' group.dat &&
ln -s '$count' count.dat &&
ln -s '$name' name.dat &&

echo 'parsimony(
    tree=tree.dat,
    iters=$iters,
    group=group.dat,
    #if $groups:
        groups=${ str($groups).replace(",","-") },
    #end if
    #if $name:
        name=name.dat,
    #end if
    #if $count:
        count=count.dat,
    #end if
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    
None
False
Functional tests
name inputs outputs required files
Test-1 tree: treetest.tre
group: treetest.groups
groups: ['green', 'orange']
name: treetest.names
iters: 1000
savelog: True
name: value
name: value
name: value
treetest.tre
treetest.groups
treetest.names
value