| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.36.1.0 |
| mothur_make_biom |
| 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 '$otu' otu.dat &&
ln -s '$constaxonomy' constaxonomy.dat &&
ln -s '$metadata' metadata.dat &&
#if $picrustc.use == "yes":
ln -s '$picrustc.picrust' picrustc.picrust.dat &&
ln -s '$picrustc.reftax' picrustc.reftax.dat &&
#end if
echo 'make.biom(
shared=otu.dat,
#if $constaxonomy:
constaxonomy=constaxonomy.dat,
#end if
#if $label:
label=${ str($label).replace(",","-") },
#end if
#if $groups:
groups=${ str($groups).replace(",","-") },
#end if
#if $metadata:
metadata=metadata.dat,
#end if
#if $picrustc.use == "yes":
picrust=picrustc.picrust.dat,
reftaxonomy=picrustc.reftax.dat,
#end if
matrixtype=$matrixtype
)'
| 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 groups: forest label: ['0.36', '0.38', '0.41'] savelog: True |
name: value |
amazon.an.shared value |
| Test-3 |
otu: final.tx.1.subsample.1.pick.shared constaxonomy: final.tx.1.cons.taxonomy metadata: metadata savelog: True |
name: value |
final.tx.1.subsample.1.pick.shared final.tx.1.cons.taxonomy metadata value |