Repository revision
10:5d8809423177

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

Classify.tree tool metadata
Miscellaneous
Classify.tree
Get a consensus taxonomy for each node on a tree
mothur_classify_tree
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_tree/mothur_classify_tree/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_classify_tree/mothur_classify_tree/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_tree/mothur_classify_tree/1.36.1.0
mothur_classify_tree
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 '$tree' tree.dat &&
ln -s '$name' name.dat &&
ln -s '$group' group.dat &&
ln -s '$taxonomy' taxonomy.dat &&

echo 'classify.tree(
    tree=tree.dat,
    #if $name
        name=name.dat,
    #end if
    #if $group:
        group=group.dat,
    #end if
    taxonomy=taxonomy.dat
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
None
False
Functional tests
name inputs outputs required files
Test-1 taxonomy: abrecovery.pds.wang.taxonomy
tree: treetest.tre
savelog: True
 name: value
name: value
name: value
 abrecovery.pds.wang.taxonomy
treetest.tre
value