| 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 |