| Miscellaneous |
| 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
| 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 |