Repository revision
9:dbb1bc225df1

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

Get.otus tool metadata
Miscellaneous
Get.otus
Get otus containing sequences from specified groups
mothur_get_otus
toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_otus/mothur_get_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_get_otus/mothur_get_otus/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_otus/mothur_get_otus/1.36.1.0
mothur_get_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 '$accnos' accnos.dat &&
#if $list:
    ln -s '$list' list.dat &&
#end if
#if $shared:
    ln -s '$shared' shared.dat &&
#end if
#if $constaxonomy:
    ln -s '$constaxonomy' constaxonomy.dat &&
#end if
#if $corraxes:
    ln -s '$corraxes' corraxes.dat &&
#end if
#if $otucorr:
    ln -s '$otucorr' otucorr.dat &&
#end if

echo 'get.otus(
    #if $list
        list=list.dat,
    #end if
    #if $shared
        shared=shared.dat,
    #end if
    #if $corraxes:
        corraxes=corraxes.dat,
    #end if
    #if $otucorr:
        otucorr=otucorr.dat,
    #end if
    #if $constaxonomy
        constaxonomy=constaxonomy.dat,
    #end if
    accnos=accnos.dat
    #if $labelsource.label:
        ,label=${ str($labelsource.label).replace(",","-") }
    #end if
)'
| 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.otus.accnos
list: amazon.an.list
savelog: True
name: value
name: value
amazon.otus.accnos
amazon.an.list
value
Test-2 accnos: amazon.otus.accnos
shared: amazon.an.shared
otucorr: amazon.an.0.03.pearson.otu.corr
labelsource|label: 0.03
labelsource|source: shared
savelog: True
name: value
name: value
amazon.otus.accnos
amazon.an.shared
amazon.an.0.03.pearson.otu.corr
value