comparison mothur/tools/mothur/hcluster.xml @ 2:e990ac8a0f58

Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository

1:fcc0778f6987

<tool id="mothur_hcluster" name="Hcluster" version="1.16.0">
 <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='hcluster'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.[fna]n\.sabund$:'$sabund,'^\S+\.[fna]n\.rabund$:'$rabund,'^\S+\.[fna]n\.list$:'$otulist

  #end if
  #if len($method.__str__) > 0:
   --method=$method
  #end if
  #if float($cutoff.__str__) > 0.0:
   --READ_cutoff=$cutoff
  #end if
  #if len($precision.__str__) > 0:
   --READ_precision=$precision
  #end if
  $hard
  $sorted
  $showabund
 </command>

   <option value="100000">.00001</option>
   <option value="1000000">.000001</option>
  </param>

  <param name="method" type="select" label="method - Select a Clustering Method" help="">
   <option value="furthest" selected="true">Furthest neighbor</option>
   <option value="nearest">Nearest neighbor</option>
   <option value="average">Average neighbor</option>
   <option value="weighted">Weighted</option>
  </param>
  <param name="sorted" type="boolean" checked="false" truevalue="--sorted=true" falsevalue="" label="sorted - The input matrix is already sorted" 
                 help=""/>
  <param name="showabund" type="boolean" checked="true" truevalue="" falsevalue="--showabund=false" label="showabund - Verbose ouput" 

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

**Command Documenation**

The cluster_ command assign sequences to OTUs (Operational Taxonomy Unit). 

.. _cluster: http://www.mothur.org/wiki/Cluster


 </help>
</tool>

2:e990ac8a0f58

<tool id="mothur_hcluster" name="Hcluster" version="1.19.0">
 <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='hcluster'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.[fna]n\.sabund$:'$sabund,'^\S+\.[fna]n\.rabund$:'$rabund,'^\S+\.[fna]n\.list$:'$otulist

  #end if
  #if len($method.__str__) > 0:
   --method=$method
  #end if
  #if float($cutoff.__str__) > 0.0:
   --cutoff=$cutoff
  #end if
  #if len($precision.__str__) > 0:
   --precision=$precision
  #end if
  $hard
  $sorted
  $showabund
 </command>

   <option value="100000">.00001</option>
   <option value="1000000">.000001</option>
  </param>

  <param name="method" type="select" label="method - Select a Clustering Method" help="">
   <option value="average" selected="true">Average neighbor</option>
   <option value="nearest">Nearest neighbor</option>
   <option value="furthest">Furthest neighbor</option>
   <option value="weighted">Weighted</option>
  </param>
  <param name="sorted" type="boolean" checked="false" truevalue="--sorted=true" falsevalue="" label="sorted - The input matrix is already sorted" 
                 help=""/>
  <param name="showabund" type="boolean" checked="true" truevalue="" falsevalue="--showabund=false" label="showabund - Verbose ouput" 

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

**Command Documenation**

The hcluster_ command assign sequences to OTUs (Operational Taxonomy Unit).  The assignment is based on a phylip-formatted_distance_matrix_ or a  column-formatted_distance_matrix_ and name_ file.  It generates a list_, a sabund_ (Species Abundance), and a rabund_ (Relative Abundance) file. 

.. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
.. _column-formatted_distance_matrix: http://www.mothur.org/wiki/Column-formatted_distance_matrix 
.. _name: http://www.mothur.org/wiki/Name_file
.. _list: http://www.mothur.org/wiki/List_file
.. _rabund: http://www.mothur.org/wiki/Rabund_file
.. _sabund: http://www.mothur.org/wiki/Sabund_file
.. _hcluster: http://www.mothur.org/wiki/Hcluster


 </help>
</tool>