| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_communitytype/mothur_get_communitytype/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_communitytype/mothur_get_communitytype/1.36.1.0 |
| mothur_get_communitytype |
| 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' shared.dat &&
echo 'get.communitytype(
shared=shared.dat,
#if $label:
label=${ str($label).replace(",","-") },
#end if
#if $groups:
groups=${ str($groups).replace(",","-") },
#end if
method=$m.method,
#if $m.method == 'kmeans' or $m.method == 'pams':
calc=$m.calc,
iters=$m.iters,
#end if
#if int($subsample) == 0:
subsample=T,
#elif int($subsample) > 0:
subsample=$subsample,
#end if
minpartitions=$minpartitions,
maxpartitions=$maxpartitions,
optimizegap=$optimizegap,
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: final.tx.1.subsample.1.pick.shared savelog: True |
name: value name: value name: value name: value name: value |
final.tx.1.subsample.1.pick.shared value |
| Test-2 |
otu: final.tx.1.subsample.1.pick.shared label: 1 groups: ['F003D000', 'F003D002', 'F003D006', 'F003D008', 'F003D142'] m|calc: manhattan m|iters: 100 m|method: kmeans maxpartitions: 4 subsample: 0 savelog: True |
name: value name: value name: value |
final.tx.1.subsample.1.pick.shared value |