Galaxy |

Summary.shared tool metadata

Miscellaneous

Name: Summary.shared

Description: Summary of calculator values for OTUs

Id: mothur_summary_shared

Guid: toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_shared/mothur_summary_shared/1.39.5.0

Version: 1.39.5.0

Version command string: mothur "#help()" | sed '7q;d' | cut -d" " -f2

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_shared/mothur_summary_shared/1.39.5.0 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_shared/mothur_summary_shared/1.36.1.0

mothur_summary_shared

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

mothur

1.39.5

package

Additional information about this tool

Command:

set -o pipefail; export TERM=vt100; 

## create symlinks to input datasets
ln -s '$otu' otu.dat &&

echo 'summary.shared(
    shared=otu.dat,
    #if $groups:
        label=${ str($label).replace(",","-") },
    #end if
    #if $label:
        groups=${ str($groups).replace(",","-") },
    #end if
    #if $calc:
        calc=${ str($calc).replace(",","-") },
    #end if
    all=$all,
    distance=$distance,
    #if $subsample.use == "yes":
        #if $subsample.subsample:
            subsample=$subsample.subsample,
        #else
            subsample=T,
        #end if
        #if $subsample.iters:
            iters=$subsample.iters,
        #end if
    #end if
    output=$output,
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log

Interpreter: None

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-1

otu: amazon.an.shared
savelog: True

name: value
name: value

amazon.an.shared
value

Test-2

otu: amazon.mothur.shared
subsample|subsample: 10
subsample|iters: 42
subsample|use: yes
savelog: True

name: value
name: value

amazon.mothur.shared
value

Test-3

otu: amazon.an.shared
label: ['0.05', '0.22', '0.32']
groups: ['forest', 'pasture']
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
name: value

amazon.an.shared
value

Test-4

otu: amazon.an.shared
calc: sorclass
distance: True
savelog: True

name: value
name: value

amazon.an.shared
value