| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_sort_seqs/mothur_sort_seqs/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_sort_seqs/mothur_sort_seqs/1.36.1.0 |
| mothur_sort_seqs |
| 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 '$fasta_in' fasta_in.dat &&
ln -s '$qfile_in' qfile_in.dat &&
ln -s '$flow_in' flow_in.dat &&
ln -s '$name_in' name_in.dat &&
ln -s '$group_in' group_in.dat &&
ln -s '$tax_in' tax_in.dat &&
ln -s '$accnos' accnos.dat &&
ln -s '$count' count.dat &&
echo 'sort.seqs(
#if $fasta_in:
fasta=fasta_in.dat,
#end if
#if $qfile_in:
qfile=qfile_in.dat,
#end if
#if $flow_in:
flow=flow_in.dat,
#end if
#if $name_in:
name=name_in.dat,
#end if
#if $group_in:
group=group_in.dat,
#end if
#if $tax_in:
taxonomy=tax_in.dat,
#end if
#if $accnos:
accnos=accnos.dat,
#end if
#if $count:
count=count.dat,
#end if
large=$large
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
fasta_in: amazon.fasta savelog: True |
name: value name: value |
amazon.fasta value |
| Test-2 |
qfile_in: Mock_S280_L001_R1_001_small.trim.contigs.qual savelog: True |
name: value name: value |
Mock_S280_L001_R1_001_small.trim.contigs.qual value |
| Test-3 |
group_in: amazon.groups savelog: True |
name: value name: value |
amazon.groups value |
| Test-4 |
fasta_in: amazon.fasta count: amazon.count_table savelog: True |
name: value name: value |
amazon.fasta amazon.count_table value |
| Test-5 |
fasta_in: amazon.fasta qfile_in: Mock_S280_L001_R1_001_small.trim.contigs.qual group_in: amazon.groups savelog: True |
name: value name: value name: value name: value |
amazon.fasta Mock_S280_L001_R1_001_small.trim.contigs.qual amazon.groups value |