| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_sens_spec/mothur_sens_spec/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_sens_spec/mothur_sens_spec/1.36.1.0 |
| mothur_sens_spec |
| 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 '$otu' otu.dat &&
ln -s '$matrix.dist' matrix.dist.dat &&
#if str($matrix.method_name.method) == "count" :
ln -s '$matrix.method_name.count' matrix.method_name.count.dat &&
#else
ln -s '$matrix.method_name.names' matrix.method_name.names.dat &&
#end if
echo 'sens.spec(
list=otu.dat,
#if str($matrix.format) == "phylip":
phylip=matrix.dist.dat,
#else
column=matrix.dist.dat,
#end if
#if str($matrix.method_name.method) == "count" :
count=matrix.method_name.count.dat,
#else
names=matrix.method_name.names.dat,
#end if
#if $label:
label=${ str($label).replace(",","-") },
#end if
#if $label:
label=${ str($label).replace(",","-") },
#end if
precision=$precision,
cutoff=$cutoff
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
matrix|dist: amazon.dist matrix|method_name|count: amazon.count_table otu: amazon.an.list savelog: True |
name: value name: value |
amazon.dist amazon.count_table amazon.an.list value |
| Test-2 |
matrix|dist: amazon.dist matrix|method_name|count: amazon.count_table otu: amazon.an.list label: ['0.03', '0.05', '0.22'] cutoff: 0.10 savelog: True |
name: value name: value |
amazon.dist amazon.count_table amazon.an.list value |