| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_sabund/mothur_get_sabund/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_sabund/mothur_get_sabund/1.36.1.0 |
| mothur_get_sabund |
| 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 '$otu' otu.dat &&
ln -s '$count' count.dat &&
echo 'get.sabund(
#if $label:
label=${ str($label).replace(",","-") },
#end if
#if $count:
count=count.dat,
#end if
#if $otu.is_of_type("mothur.list"):
list=otu.dat
#elif $otu.is_of_type("mothur.rabund"):
rabund=otu.dat
#end if
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
otu: amazon.an.rabund savelog: True |
name: value name: value |
amazon.an.rabund value |
| Test-2 |
otu: amazon.an.list label: ['0.03', '0.05'] savelog: True |
name: value name: value |
amazon.an.list value |