| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.36.1.0 |
| mothur_cluster_split |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| mothur | 1.39.5 | package |
| vsearch | 2.6.0 | package |
| Additional information about this tool |
set -o pipefail; export TERM=vt100;
## create symlinks to input datasets
#if $splitby.splitmethod == "distance":
ln -s '$splitby.matrix.dist' splitby.matrix.dist.dat &&
ln -s '$splitby.matrix.nameOrCount' splitby.matrix.nameOrCount.dat &&
#elif $splitby.splitmethod == "classify":
ln -s '$splitby.dist' splitby.dist.dat &&
ln -s '$splitby.nameOrCount' splitby.nameOrCount.dat &&
ln -s '$splitby.taxonomy' splitby.taxonomy.dat &&
#elif $splitby.splitmethod == "fasta":
ln -s '$splitby.fasta' splitby.fasta.dat &&
ln -s '$splitby.nameOrCount' splitby.nameOrCount.dat &&
ln -s '$splitby.taxonomy' splitby.taxonomy.dat &&
#end if
echo 'cluster.split(
splitmethod=$splitby.splitmethod,
#if $splitby.splitmethod == "distance":
#if $splitby.matrix.format == "column":
column=splitby.matrix.dist.dat,
#if $splitby.matrix.nameOrCount.is_of_type("mothur.names"):
name=splitby.matrix.nameOrCount.dat,
#elif $splitby.matrix.nameOrCount.is_of_type("mothur.count_table"):
count=splitby.matrix.nameOrCount.dat,
#end if
#elif $splitby.matrix.format == "phylip":
phylip=splitby.matrix.dist.dat,
#if $splitby.matrix.nameOrCount:
#if $splitby.matrix.nameOrCount.is_of_type("mothur.names"):
name=splitby.matrix.nameOrCount.dat,
#elif $splitby.matrix.nameOrCount.is_of_type("mothur.count_table"):
count=splitby.matrix.nameOrCount.dat,
#end if
#end if
#end if
#elif $splitby.splitmethod == "classify":
column=splitby.dist.dat,
taxonomy=splitby.taxonomy.dat,
#if $splitby.nameOrCount.is_of_type("mothur.names"):
name=splitby.nameOrCount.dat,
#elif $splitby.nameOrCount.is_of_type("mothur.count_table"):
count=splitby.nameOrCount.dat,
#end if
#if $splitby.taxlevel:
taxlevel=$splitby.taxlevel,
#end if
#elif $splitby.splitmethod == "fasta":
fasta=splitby.fasta.dat,
taxonomy=splitby.taxonomy.dat,
#if $splitby.nameOrCount.is_of_type("mothur.names"):
name=splitby.nameOrCount.dat,
#elif $splitby.nameOrCount.is_of_type("mothur.count_table"):
count=splitby.nameOrCount.dat,
#end if
#if $splitby.taxlevel:
taxlevel=$splitby.taxlevel,
#end if
classic=$splitby.classic,
#end if
method=$splitby.condmethod.method,
#if $splitby.condmethod.method == "opti":
metric=$splitby.condmethod.metric,
initialize=$splitby.condmethod.initialize,
delta=$splitby.condmethod.delta,
iters=$splitby.condmethod.iters,
#end if
#if float($cutoff) > 0.0:
cutoff=$cutoff,
#end if
#if $precision
precision=$precision,
#end if
large=$large,
cluster=$cluster,
runsensspec=$runsensspec,
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 |
splitby|matrix|dist: 98_sq_phylip_amazon.dist splitby|matrix|format: phylip splitby|condmethod|method: average splitby|splitmethod: distance savelog: True |
name: value name: value name: value name: value |
98_sq_phylip_amazon.dist value |
| Test-2 |
splitby|matrix|dist: 98_sq_phylip_amazon.dist splitby|matrix|format: phylip splitby|condmethod|method: average splitby|splitmethod: distance cluster: False savelog: True |
name: value name: value |
98_sq_phylip_amazon.dist value |
| Test-3 |
splitby|dist: amazon.pair.dist splitby|taxonomy: amazon.wang.wang.taxonomy splitby|nameOrCount: amazon.names splitby|condmethod|method: average splitby|splitmethod: classify savelog: True |
name: value name: value name: value name: value |
amazon.pair.dist amazon.wang.wang.taxonomy amazon.names value |
| Test-4 |
splitby|dist: amazon.pair.dist splitby|taxonomy: amazon.wang.wang.taxonomy splitby|nameOrCount: amazon.count_table splitby|condmethod|method: average splitby|splitmethod: classify savelog: True |
name: value name: value |
amazon.pair.dist amazon.wang.wang.taxonomy amazon.count_table value |
| Test-5 |
splitby|fasta: amazon.align_head splitby|taxonomy: amazon.align_head.wang.taxonomy splitby|nameOrCount: amazon.align_head.names splitby|condmethod|method: average splitby|splitmethod: fasta cutoff: 9999 savelog: True |
name: value name: value name: value name: value |
amazon.align_head amazon.align_head.wang.taxonomy amazon.align_head.names value |
| Test-6 |
splitby|fasta: amazon.align_head splitby|taxonomy: amazon.align_head.wang.taxonomy splitby|nameOrCount: amazon.align_head.names splitby|condmethod|method: agc splitby|splitmethod: fasta savelog: True |
name: value name: value name: value name: value |
amazon.align_head amazon.align_head.wang.taxonomy amazon.align_head.names value |
| Test-7 |
splitby|matrix|dist: 98_sq_phylip_amazon.dist splitby|matrix|format: phylip splitby|condmethod|method: opti splitby|splitmethod: distance savelog: True |
name: value name: value name: value name: value name: value |
98_sq_phylip_amazon.dist value |