| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.36.1.0 |
| mothur_classify_otu |
| 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 '$otu' otu.dat &&
ln -s '$tax.taxonomy' tax.taxonomy.dat &&
ln -s '$name' name.dat &&
ln -s '$count' count.dat &&
ln -s '$group' group.dat &&
echo 'classify.otu(
list=otu.dat,
taxonomy=tax.taxonomy.dat,
#if $name:
name=name.dat,
#end if
#if $count:
count=count.dat,
#end if
#if $label:
label=${ str($label).replace(",","-") },
#end if
#if $group:
group=group.dat,
#end if
basis=$basis,
probs=$probs,
persample=$persample,
cutoff=$cutoff,
relabund=$relabund,
output=$output,
printlevel=$printlevel
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
otu: amazon.an.list tax|taxonomy: abrecovery.pds.wang.taxonomy tax|source: hist savelog: True |
name: value |
amazon.an.list abrecovery.pds.wang.taxonomy value |
| Test-2 |
otu: amazon.an.list name: amazon1.names tax|taxonomy: abrecovery.pds.wang.taxonomy tax|source: hist label: ['unique', '0.05', '0.18'] savelog: True |
name: value |
amazon.an.list amazon1.names abrecovery.pds.wang.taxonomy value |
| Test-3 |
otu: amazon.an.list count: amazon1.count_table tax|taxonomy: abrecovery.pds.wang.taxonomy tax|source: hist label: ['unique', '0.05', '0.18'] savelog: True |
name: value |
amazon.an.list amazon1.count_table abrecovery.pds.wang.taxonomy value |
| Test-4 |
otu: amazon.an.list tax|taxonomy: abrecovery.pds.wang.taxonomy tax|source: hist label: ['unique', '0.05', '0.18'] group: amazon.groups savelog: True |
name: value |
amazon.an.list abrecovery.pds.wang.taxonomy amazon.groups value |