| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_create_database/mothur_create_database/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_create_database/mothur_create_database/1.36.1.0 |
| mothur_create_database |
| 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 '$otu' otu.dat &&
ln -s '$repfasta' repfasta.dat &&
ln -s '$nameOrCount' nameOrCount.dat &&
ln -s '$constaxonomy' constaxonomy.dat &&
ln -s '$group' group.dat &&
echo 'create.database(
#if $otu.is_of_type("mothur.list"):
list=otu.dat
#elif $otu.is_of_type("mothur.shared"):
shared=otu.dat
#end if
,repfasta=repfasta.dat
#if $nameOrCount.is_of_type("mothur.names"):
,repname=nameOrCount.dat
#elif $nameOrCount.is_of_type("mothur.count_table"):
,count=nameOrCount.dat
#end if
,constaxonomy=constaxonomy.dat
#if $group:
,group=group.dat
#end if
#if $label:
,label=$label
#end if
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
otu: cd-test.list repfasta: cd-test.repfasta nameOrCount: cd-test.repname constaxonomy: cd-test.constaxonomy label: unique savelog: True |
name: value name: value |
cd-test.list cd-test.repfasta cd-test.repname cd-test.constaxonomy value |
| Test-2 |
otu: cd-test.list repfasta: cd-test.repfasta nameOrCount: cd-test.count_table constaxonomy: cd-test.constaxonomy label: unique savelog: True |
name: value name: value |
cd-test.list cd-test.repfasta cd-test.count_table cd-test.constaxonomy value |