| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_pairwise_seqs/mothur_pairwise_seqs/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_pairwise_seqs/mothur_pairwise_seqs/1.36.1.0 |
| mothur_pairwise_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 '$fasta' fasta.dat &&
echo 'pairwise.seqs(
fasta=fasta.dat,
align=$align,
#if $calc:
calc=$calc,
#end if
$countends
#if float($cutoff) > 0.0:
cutoff=$cutoff,
#end if
#if $scoring.setby == "user":
match=$scoring.match,
mismatch=$scoring.mismatch,
gapopen=$scoring.gapopen,
gapextend=$scoring.gapextend,
#end if
#if $output:
output=$output,
#end if
processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
fasta: amazon.unique.fasta align: needleman calc: countends: True cutoff: 0.0 scoring|setby: default output: savelog: True |
name: value name: value |
amazon.unique.fasta value |
| Test-2 |
fasta: amazon.unique.fasta align: gotoh calc: onegap countends: False cutoff: 0.01 scoring|match: 2 scoring|mismatch: -1 scoring|gapopen: -2 scoring|gapextend: -1 scoring|setby: user output: lt savelog: True |
name: value name: value |
amazon.unique.fasta value |