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 |