annotate mothur/tools/mothur/cluster.xml @ 36:040410b8167e default tip

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

<tool id="mothur_cluster" name="Cluster" version="1.28.0">
 <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='cluster'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.[fna]n\.sabund$:'$sabund,'^\S+\.[fna]n\.rabund$:'$rabund,'^\S+\.[fna]n\.list$:'$otulist
  --outputdir='$logfile.extra_files_path'
  #if $matrix.format == "column":
   --column=$matrix.dist
   --name=$matrix.name
  #elif $matrix.format == "phylip":
   --phylip=$matrix.dist
   #if $matrix.name.__str__ != "None" and len($matrix.name.__str__) > 0:
    --name=$matrix.name
   #end if
  #end if
  #if $count.__str__ != "None" and len($count.__str__) > 0:
    --count=$count
  #end if
  $sim
  #if float($cutoff.__str__) > 0.0:
   --cutoff=$cutoff
  #end if
  $hard
  #if len($precision.__str__) > 0:
   --precision=$precision
  #end if
  #if len($method.__str__) > 0:
   --method=$method
  #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="column - Distance Matrix"/>
    <param name="name" type="data" format="names" label="name - Sequences Name reference"/>
   </when>
   <when value="phylip">
    <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
    <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
   </when>
  </conditional>
  <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
  <!-- ? conditional - to hide complexity -->
  <param name="method" type="select" label="method - Select a Clustering Method" help="">
   <option value="furthest">Furthest neighbor</option>
   <option value="nearest">Nearest neighbor</option>
   <option value="average" selected="true">Average neighbor</option>
   <option value="weighted">Weighted</option>
  </param>
  <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" 
                 help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
  <param name="hard" type="boolean" checked="true" truevalue="--hard=true" falsevalue="--hard=false" label="hard - Use hard cutoff instead of rounding" 
                 help=""/>
  <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values"
                 help="Set higher precision for longer genome scale sequence lengths">
   <option value="10">.1</option>
   <option value="100" selected="true">.01</option>
   <option value="1000">.001</option>
   <option value="10000">.0001</option>
   <option value="100000">.00001</option>
   <option value="1000000">.000001</option>
  </param>
  <param name="sim" type="boolean" checked="false" truevalue="--sim=true" falsevalue="" label="sim - Matrix values are Similary instead of Distance" 
                 help=""/>

 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
  <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
  <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/>
 </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 cluster_ 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
.. _cluster: http://www.mothur.org/wiki/Cluster


 </help>
</tool>