Repository revision
10:9ac808d4e0b5

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

Remove.rare tool metadata
Miscellaneous
Remove.rare
Remove rare OTUs
mothur_remove_rare
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_rare/mothur_remove_rare/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_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
    
None
False
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