Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_rare/mothur_remove_rare/1.39.5.0 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_rare/mothur_remove_rare/1.36.1.0 |
mothur_remove_rare |
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 '$input.otu' input_otu.dat && #if $input.source == 'list': ln -s '$input.group' input.group.dat && ln -s '$input.count' input.count.dat && #end if echo 'remove.rare( #if $input.otu.is_of_type("mothur.rabund"): rabund=input_otu.dat, #elif $input.otu.is_of_type("mothur.sabund"): sabund=input_otu.dat, #elif $input.otu.is_of_type("mothur.list"): list=input_otu.dat, #if $input.group: group=input.group.dat, #end if #if $input.groups: groups=${ str($input.groups).replace(",","-") }, #end if #if $input.count: count=input.count.dat, #end if #elif $input.otu.is_of_type("mothur.shared"): shared=input_otu.dat, bygroup=$input.bygroup, #if $input.groups: groups=${ str($input.groups).replace(",","-") }, #end if #end if #if $input.label: label=${ str($input.label).replace(",","-") }, #end if nseqs=$nseqs )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log
Functional tests |
name | inputs | outputs | required files |
Test-1 |
input|otu: amazon.an.list input|source: list savelog: True |
name: value name: value |
amazon.an.list value |
Test-2 |
input|otu: amazon.an.list input|group: amazon.groups input|groups: ['forest', 'pasture'] input|source: list savelog: True |
name: value name: value name: value |
amazon.an.list amazon.groups value |
Test-3 |
input|otu: amazon.an.shared input|source: shared savelog: True |
name: value |
amazon.an.shared value |
Test-4 |
input|otu: amazon.an.shared input|groups: ['forest', 'pasture'] input|bygroup: True input|label: ['0.05', '0.22', '0.41'] input|source: shared savelog: True |
name: value |
amazon.an.shared value |
Test-5 |
input|otu: amazon.an.sabund input|source: default savelog: True |
name: value name: value |
amazon.an.sabund value |