Repository revision
9:43e2715e98c9

Repository 'mothur_tree_shared'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared

Tree.shared tool metadata
Miscellaneous
Tree.shared
Generate a newick tree for dissimilarity among groups
mothur_tree_shared
toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0
1.39.5.0
mothur "#help()" | sed '7q;d' | cut -d" " -f2
True
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
    
None
False
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