Repository revision
10:1c6dadf7bc72

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

Indicator tool metadata
Miscellaneous
Indicator
Identify indicator "species" for nodes on a tree
mothur_indicator
toolshed.g2.bx.psu.edu/repos/iuc/mothur_indicator/mothur_indicator/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_indicator/mothur_indicator/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_indicator/mothur_indicator/1.36.1.0
mothur_indicator
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 '$otu' otu.dat &&
#if $withdesign.tree:
    ln -s '$withdesign.tree' withdesign.tree.dat &&
#end if
#if $withdesign.havedesign == "yes":
    ln -s '$withdesign.design' withdesign.design.dat &&
#end if

echo 'indicator(
    #if $withdesign.tree:
        tree=withdesign.tree.dat,
    #end if
    #if $otu.is_of_type("mothur.relabund"):
        relabund=otu.dat,
    #elif $otu.is_of_type("mothur.shared"):
        shared=otu.dat,
    #end if
    #if $label:
        label=${ str($label).replace(",","-") },
    #end if
    #if $withdesign.groups:
        groups=${ str($withdesign.groups).replace(",","-") },
    #end if
    #if $withdesign.havedesign == "yes":
        design=withdesign.design.dat,
    #end if
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    
None
False
Functional tests
name inputs outputs required files
Test-1 otu: amazon.an.shared
label: 0.03
withdesign|design: toymothur.design2
withdesign|groups: ['tardis', 'dalek']
withdesign|havedesign: yes
savelog: True
name: value
name: value
amazon.an.shared
toymothur.design2
value
Test-2 otu: amazon.an.shared
withdesign|design: toymothur.design2
withdesign|groups: tardis
withdesign|havedesign: yes
savelog: True
name: value
name: value
amazon.an.shared
toymothur.design2
value
Test-3 otu: amazon.an.shared
withdesign|tree: amazon.an.jclass.unique.tre
withdesign|groups: ['forest', 'pasture']
withdesign|havedesign: no
savelog: True
name: value
name: value
name: value
amazon.an.shared
amazon.an.jclass.unique.tre
value
Test-4 otu: amazon.an.shared
withdesign|tree: amazon.an.jclass.unique.tre
withdesign|groups: forest
withdesign|havedesign: no
savelog: True
name: value
name: value
name: value
amazon.an.shared
amazon.an.jclass.unique.tre
value