| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_collect_single/mothur_collect_single/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_collect_single/mothur_collect_single/1.36.1.0 |
| mothur_collect_single |
| 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.single(
#if $otu.is_of_type("mothur.rabund"):
rabund=otu.dat,
#elif $otu.is_of_type("mothur.sabund"):
sabund=otu.dat,
#elif $otu.is_of_type("mothur.shared"):
shared=otu.dat,
#elif $otu.is_of_type("mothur.list"):
list=otu.dat,
#end if
#if $label:
label=${ str($label).replace(",","-") },
#end if
calc=${ str($calc).replace(",","-") },
abund=$abund,
freq=$freq
)'
| 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.list savelog: True |
name: value |
amazon.an.list value |
| Test-2 |
otu: amazon.an.sabund label: ['0.36', '0.38', '0.41'] calc: ['ace', 'bootstrap', 'chao', 'jack', 'sobs', 'simpsoneven', 'shannoneven', 'heip', 'smithwilson', 'bergerparker', 'coverage', 'goodscoverage', 'simpson', 'invsimpson', 'qstat', 'shannon', 'npshannon', 'boneh', 'efron', 'shen', 'solow', 'logseries', 'geometric', 'bstick', 'nseqs'] savelog: True |
name: value |
amazon.an.sabund value |