| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_clearcut/mothur_clearcut/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_clearcut/mothur_clearcut/1.36.1.0 |
| mothur_clearcut |
| 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 '$input.infile' input.infile.dat &&
echo 'clearcut(
#if $input.source == "dna":
fasta=input.infile.dat,
DNA=true,
#elif $input.source == "aa":
fasta=input.infile.dat,
protein=true,
#elif $input.source == "phylip":
phylip=input.infile.dat,
#end if
#if $matrixout == "true":
matrixout=matrixout.dist,
#end if
#if $seed:
seed=$seed,
#end if
ntrees=$ntrees,
norandom=$norandom,
shuffle=$shuffle,
expblen=$expblen,
expdist=$expdist,
neighbor=$neighbor
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input|infile: env.dist input|source: phylip savelog: True |
name: value name: value |
env.dist value |
| Test-2 |
input|infile: env.dist input|source: phylip ntrees: 3 norandom: True shuffle: True neighbor: False expblen: True expdist: True matrixout: True savelog: True |
name: value name: value name: value |
env.dist value |
| Test-3 |
input|infile: amazon.align_head input|source: dna matrixout: True savelog: True |
name: value name: value name: value |
amazon.align_head value |