Repository revision
9:0e73681a7cdc

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

Remove.otus tool metadata
Miscellaneous
Remove.otus
Removes OTUs from various file formats
mothur_remove_otus
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_otus/mothur_remove_otus/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_otus/mothur_remove_otus/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_otus/mothur_remove_otus/1.36.1.0
mothur_remove_otus
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 '$infile.otu' infile.otu.dat &&
ln -s '$accnos' accnos.dat &&

echo 'remove.otus(
    #if $infile.otu.is_of_type("mothur.cons.taxonomy"):
        constaxonomy=infile.otu.data,
    #end if
    #if $infile.otu.is_of_type("mothur.otu.corr"):
        otucorr=infile.otu.dat,
    #end if
    #if $infile.otu.is_of_type("mothur.axes"):
        corraxes=infile.otu.dat,
    #end if
    #if $infile.otu.is_of_type("mothur.list"):
        list=infile.otu.dat,
    #end if
    #if $infile.otu.is_of_type("mothur.shared"):
        shared=infile.otu.dat,
    #end if
    #if $infile.intype == "in_shared" and $infile.label:
        label=${ str($infile.label).replace(",","-") },
    #end if
    accnos=accnos.dat
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    
None
False
Functional tests
name inputs outputs required files
Test-1 accnos: amazon.accnos.otulabels
infile|otu: amazon.an.list
infile|label: 0.22
infile|intype: in_shared
savelog: True
name: value
name: value
amazon.accnos.otulabels
amazon.an.list
value
Test-2 accnos: amazon.accnos.otulabels
infile|otu: amazon.pcoa.axes
infile|intype: in_other
savelog: True
name: value
name: value
amazon.accnos.otulabels
amazon.pcoa.axes
value