| 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 |