| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_split_abund/mothur_split_abund/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_split_abund/mothur_split_abund/1.36.1.0 |
| mothur_split_abund |
| 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 '$fasta' fasta.dat &&
ln -s '$search.input' search_input.dat &&
#if $split.dosplit == "yes":
ln -s '$split.group' split_group.dat &&
#end if
echo 'split.abund(
fasta=fasta.dat,
#if $search.type == "list":
list=search_input.dat,
#if $search.label:
label=${ str($search.label).replace(",","-") },
#end if
#elif $search.type == "name":
name=search_input.dat,
#else
count=search_input.dat,
#end if
#if $split.dosplit == "yes":
#if $split.group:
group=split_group.dat,
#end if
#if $split.groups:
groups=${ str($split.groups).replace(",","-") },
#end if
#end if
accnos=$accnos,
cutoff=$cutoff
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
fasta: amazon.fasta cutoff: 1 search|input: amazon.count_table search|type: count accnos: True savelog: True |
name: value name: value name: value name: value name: value name: value name: value |
amazon.fasta amazon.count_table value |
| Test-2 |
fasta: amazon.fasta cutoff: 1 search|input: amazon.names search|type: name accnos: True savelog: True |
name: value name: value name: value name: value name: value name: value name: value |
amazon.fasta amazon.names value |
| Test-3 |
fasta: amazon.fasta cutoff: 1 search|input: amazon.names search|type: name split|group: amazon.groups split|groups: ['forest', 'pasture'] split|dosplit: yes accnos: True savelog: True |
name: value |
amazon.fasta amazon.names amazon.groups value |
| Test-4 |
fasta: amazon.fasta cutoff: 2 search|input: amazon.an.list search|type: list split|group: amazon.groups split|groups: ['forest', 'pasture'] split|dosplit: yes accnos: True savelog: True |
name: value |
amazon.fasta amazon.an.list amazon.groups value |
| Test-5 |
fasta: amazon.fasta cutoff: 2 search|input: amazon.an.list search|label: ['0.05', '0.22'] search|type: list split|group: amazon.groups split|groups: ['forest', 'pasture'] split|dosplit: yes accnos: True savelog: True |
name: value |
amazon.fasta amazon.an.list amazon.groups value |