view mothur/tools/mothur/libshuff.xml @ 36:040410b8167e default tip

Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.

<tool id="mothur_libshuff" name="Libshuff" version="1.20.0">
 <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='$logfile.extra_files_path'
  --phylip=$dist
  --group=$group
  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
    --groups=$groups
  #end if
  #if len($iters.__str__) > 0:
   --iters=$iters
  #end if
  $sim
  #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=$form.cutoff
   #end if
  #end if
 </command>
 <inputs>
  <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
  <param name="group" type="data" format="groups" label="group - Groups"/>
  <param name="groups" type="select" label="groups - Groups to condider" multiple="true">
   <options>
    <filter type="data_meta" ref="group" key="groups" />
   </options>
  </param>
  <param name="iters" type="integer" value="10000" label="iters - Number of iterations to try (default 10000)"/>
  <param name="sim" type="boolean" checked="false" truevalue="--sim=true" falsevalue="" label="sim - Matrix values are Similary instead of Distance" help=""/>
  <conditional name="form">
   <param name="form" type="select" label="form - Select a Clustering Method" help="">
    <option value="integral" selected="true">Integral</option>
    <option value="discrete">Discrete</option>
   </param>
   <when value="integral"/>
   <when value="discrete">
    <param name="step" type="float" value="0.0" label="step - Step size - ignored if not > 0" 
                 help="default value 0.10, smaller steps approach integral"/>
    <param name="cutoff" type="float" value="0.0" label="cutoff - Cutoff threshold - ignored if not > 0" help=""/>
   </when>
  </conditional>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${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="package" version="1.33">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>