view mothur/tools/mothur/libshuff.xml @ 1:fcc0778f6987

Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository

<tool id="mothur_libshuff" name="Libshuff" version="1.16.0">
 <description>Cramer-von Mises tests communities for the same structure</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='libshuff'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.libshuff\.summary$:'$summary,'^\S+\.libshuff\.coverage$:'$coverage
  --outputdir='$logfile.extra_files_path'
  --READ_cmd='read.dist'
  #if $matrix.format == "column":
   --READ_column=$matrix.dist
   --READ_name=$matrix.name
  #elif $matrix.format == "phylip":
   --READ_phylip=$matrix.dist
  #end if
  --READ_group=$group
  #if len($iters.__str__) > 0:
   --iters=$iters
  #end if
  #if $form == "discrete":
   #if 1.0 >= float($form.step.__str__) > 0.0:
    --step=$form.step
   #end if
   #if 1.0 >= float($cutoff.__str__) > 0.0:
    --cutoff=$form.cutoff
   #end if
  #end if
 </command>
 <inputs>
  <conditional name="matrix">
   <param name="format" type="select" label="Select a Distance Matrix Format" help="">
    <option value="column">Pairwise Column Matrix</option>
    <option value="phylip">Phylip Distance Matrix</option>
   </param>
   <when value="column">
    <param name="dist" type="data" format="pair.dist" label="read.dist(column=) - Distance Matrix"/>
    <param name="name" type="data" format="names" label="read.dist(name) - Sequences Name reference"/>
   </when>
   <when value="phylip">
    <param name="dist" type="data" format="lower.dist,square.dist" label="read.dist(phylip=) - Distance Matrix"/>
   </when>
  </conditional>
  <param name="group" type="data" format="groups" label="read.dist(group=) - Groups"/>
  <!-- ? conditional - to hide complexity -->
  <param name="iters" type="integer" value="10000" label="iters - Number of iterations to try (default 10000)"/>
  <conditional name="form">
   <param name="form" type="select" label="form - Select a Clustering Method" help="">
    <option value="integral" selected="true">Integral</option>
    <option value="discrete">Discrete</option>
   </param>
   <when value="integral"/>
   <when value="discrete">
    <param name="step" type="float" value="0.0" label="step - Step size - ignored if not > 0" 
                 help="default value 0.10, smaller steps approach integral"/>
    <param name="cutoff" type="float" value="0.0" label="cutoff - Cutoff threshold - ignored if not > 0" help=""/>
   </when>
  </conditional>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary"/>
  <data format="tabular" name="coverage" label="${tool.name} on ${on_string}: coverage"/>
 </outputs>
 <requirements>
  <requirement type="binary">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**

Mothur_, initiated by Dr. Patrick Schloss and his software development team
in the Department of Microbiology and Immunology at The University of Michigan,
provides bioinformatics for the microbial ecology community.

.. _Mothur: http://www.mothur.org/wiki/Main_Page

**Command Documenation**

The libshuff_ method is a generic test that describes whether two or more communities have the same structure using the Cramer-von Mises test statistic. The significance of the test statistic indicates the probability that the communities have the same structure by chance. Because each pairwise comparison requires two significance tests, a correction for multiple comparisons (e.g. Bonferroni's correction) must be applied.

.. _libshuff: http://www.mothur.org/wiki/Libshuff


 </help>
</tool>