| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.36.1.0 |
| mothur_rarefaction_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 'rarefaction.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,
iters=$iters,
freq=$freq,
processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
## rename output from sobs calculator to be consistent with others
#if 'sobs' in str($calc).split(','):
&& mv otu\.*rarefaction otu.r_sobs
#end if
| 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', '0.36', '0.55'] calc: ['ace', 'bootstrap', 'chao', 'jack', 'sobs', 'simpsoneven', 'shannoneven', 'heip', 'smithwilson', 'coverage', 'simpson', 'invsimpson', 'shannon', 'npshannon', 'nseqs'] savelog: True |
name: value |
amazon.an.shared value |