Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/mothur_phylo_diversity/mothur_phylo_diversity/1.39.5.0 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/mothur_phylo_diversity/mothur_phylo_diversity/1.36.1.0 |
mothur_phylo_diversity |
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 '$count' count.dat && #if $grouping.use == "yes": ln -s '$grouping.group' grouping.group.dat && #end if echo 'phylo.diversity( tree=tree.dat, #if $grouping.use == "yes": group=grouping.group.dat, #if $grouping.groups: groups=${ str($grouping.groups).replace(",","-") }, #end if #end if #if $name: name=name.dat, #end if iters=$iters, freq=$freq, scale=$scale, collect=$collect, rarefy=$rarefy, summary=$summary, #if $count: count=count.dat, #end if processors='\${GALAXY_SLOTS:-8}' )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log
Functional tests |
name | inputs | outputs | required files |
Test-1 |
tree: treetest.tre grouping|use: no savelog: True |
name: value name: value |
treetest.tre value |
Test-2 |
tree: treetest.tre grouping|group: treetest.groups grouping|groups: ['orange', 'green'] grouping|use: yes rarefy: True collect: True savelog: True |
name: value name: value name: value name: value |
treetest.tre treetest.groups value |