| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_collect_shared/mothur_collect_shared/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_collect_shared/mothur_collect_shared/1.36.1.0 |
| mothur_collect_shared |
| 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 &&
echo 'collect.shared(
shared=otu.dat,
#if $label:
label=${ str($label).replace(",","-") },
#end if
#if $calc:
calc=${ str($calc).replace(",","-") },
#end if
#if $groups:
groups=${ str($groups).replace(",","-") },
#end if
freq=$freq,
all=true
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
&& rm otu.dat ## don't want this collected into datacollection
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
otu: amazon.an.shared savelog: True |
name: value |
amazon.an.shared value |
| Test-2 |
otu: amazon.an.shared label: ['0.03', '0.05', '0.22'] groups: ['forest', 'pasture'] calc: ['sharedsobs', 'sharedchao', 'sharedace', 'anderberg', 'jclass', 'jest', 'kulczynski', 'kulczynskicody', 'kstest', 'lennon', 'ochiai', 'sorclass', 'sorest', 'whittaker', 'hamming', 'memchi2', 'memchord', 'memeuclidean', 'mempearson', 'braycurtis', 'jabund', 'morisitahorn', 'sorabund', 'thetan', 'thetayc', 'canberra', 'gower', 'hellinger', 'manhattan', 'odum', 'soergel', 'spearman', 'speciesprofile', 'structchi2', 'structchord', 'structeuclidean', 'structkulczynski', 'structpearson', 'sharednseqs'] savelog: True |
name: value |
amazon.an.shared value |