| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_coremicrobiome/mothur_get_coremicrobiome/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_coremicrobiome/mothur_get_coremicrobiome/1.36.1.0 |
| mothur_get_coremicrobiome |
| 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 'get.coremicrobiome(
#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 $groups:
,groups=${ str($groups).replace(",","-") }
#end if
#if $abundance:
,abundance=$abundance
#end if
#if $samples:
,samples=$samples
#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.shared savelog: True |
name: value |
amazon.an.shared value |
| Test-2 |
otu: amazon.an.shared label: ['0.05', '0.22', '0.45'] abundance: 30 savelog: True |
name: value |
amazon.an.shared value |