| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.36.1.0 |
| mothur_tree_shared |
| 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.dist' input_dist.dat &&
#if not $input.source == "shared":
ln -s '$input.name' input_name.dat &&
#end if
echo 'tree.shared(
#if $input.source == "shared":
shared=input_dist.dat,
#if $input.groups:
groups=${ str($input.groups).replace(",","-") },
#end if
#if $input.label:
label=${ str($input.label).replace(",","-") },
#end if
#if $input.subsampling.use == "yes":
#if $input.subsampling.subsample:
subsample=$input.subsampling.subsample,
#else
subsample=T,
#end if
#if $input.subsampling.iters:
iters="$input.subsampling.iters,
#end if
#end if
#elif $input.source == "column":
column=input_dist.dat,
name=input_name.dat,
#elif $input.source == "phylip":
phylip=input_dist.dat,
#if $input.name:
name=input_name.dat,
#end if
#else
count=input_name.dat,
#end if
#if $calc:
calc=${ str($calc).replace(",","-") },
#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 |
input|dist: env.dist input|source: phylip savelog: True |
name: value name: value |
env.dist value |
| Test-2 |
input|dist: amazon.an.shared input|subsampling|use: yes input|source: shared calc: jclass savelog: True |
name: value |
amazon.an.shared value |
| Test-3 |
input|dist: amazon.an.shared input|label: ['0.05', '0.22', '0.32'] input|groups: ['forest', 'pasture'] input|source: shared calc: ['sharedsobs', 'sharedchao', 'sharedace', 'anderberg', 'jclass', 'jest', 'kulczynski', 'kulczynskicody', 'kstest', 'lennon', 'ochiai', 'sorclass', 'sorest', 'whittaker', 'hamming', 'memchi2', 'memchord', 'memeuclidean', 'mempearson', 'braycurtis', 'jabund', 'morisitahorn', 'sorabund', 'thetan', 'thetayc', 'canberra', 'gower', 'hellinger', 'manhattan', 'odum', 'soergel', 'spearman', 'speciesprofile', 'structchi2', 'structchord', 'structeuclidean', 'structkulczynski', 'structpearson', 'sharednseqs', 'sharedobserved'] savelog: True |
name: value |
amazon.an.shared value |
| Test-4 |
input|dist: amazon.pair.dist input|name: amazon1.names input|source: column savelog: True |
name: value name: value |
amazon.pair.dist amazon1.names value |