annotate mothur/tools/mothur/clearcut.xml @ 2:e990ac8a0f58

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

<tool id="mothur_clearcut" name="Clearcut" version="1.19.0">
 <description>Generate a tree using relaxed neighbor joining</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='clearcut'
  #if $matrixout == True or $matrixout.__str__ == "true":
   --matrixout='matrixout.dist'
   --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.tre$:'$tree,'^matrixout\.dist$:'$matrix
  #else 
   --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.tre$:'$tree
  #end if
  --outputdir='$logfile.extra_files_path'
  #if $input.source == 'dna':
   --fasta=$input.fasta
   --DNA=true
  #elif $input.source == 'aa':
   --fasta=$input.fasta
   --protein=true
  #elif $input.source == 'phylip':
   --phylip=$input.dist
  #end if
  #if int($seed.__str__) >= 0:
   --seed=$seed
  #end if
  #if int($ntrees.__str__) > 1:
   --ntrees=$ntrees
  #end if
  $norandom
  $shuffle
  $neighbor
 </command>
 <inputs>
  <!-- get.relabund  relabund type should also work -->
  <conditional name="input">
   <param name="source" type="select" label="Distance Matrix">
    <option value="dna">DNA Alignment Fasta</option>
    <option value="aa">Protein Alignment Fasta</option>
    <option value="phylip">Phylip Distance Matrix</option>
   </param>
   <when value="dna">
    <param name="fasta" type="data" format="align" label="fasta - Alignment Fasta"/>
   </when>
   <when value="aa">
    <param name="fasta" type="data" format="align" label="fasta - Alignment Fasta"/>
   </when>
   <when value="phylip">
    <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
   </when>
  </conditional>
  <param name="seed" type="integer" value="-1" label="seed - Set the PRNG seed to a specific value (ignored if negative)"/>
  <param name="ntrees" type="integer" value="1" label="ntrees - the number of output trees you want clearcut to generate (ignored if &lt; 1)"/>
  <param name="norandom" type="boolean" checked="false" truevalue="--norandom=true" falsevalue="" label="norandom - Attempt joins deterministically"/>
  <param name="shuffle" type="boolean" checked="false" truevalue="--shuffle=true" falsevalue="" label="shuffle - Randomly shuffle the distance matrix"/>
  <param name="neighbor" type="boolean" checked="false" truevalue="--neighbor=true" falsevalue="" label="neighbor - Use traditional Neighbor-Joining algorithm"/>
  <param name="expblen" type="boolean" checked="false" truevalue="--expblen=true" falsevalue="" label="expblen - Use exponential notation for branch lengths"/>
  <param name="expdist" type="boolean" checked="false" truevalue="--expdist=true" falsevalue="" label="expdist - Use exponential notation for distance"/>
  <param name="matrixout" type="boolean" checked="false" truevalue="true" falsevalue="" label="matrixout - Generate a Distance Matrix"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tre" name="tree" label="${tool.name} on ${on_string}: tree" />
  <data format="lower.dist" name="matrix" label="${tool.name} on ${on_string}: Phylip Distance Matrix" >
   <filter>matrixout == True</filter>
  </data>
 </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 clearcut_ command runs clearcut

The clearcut command allows mothur users to run the clearcut_program_ from within mothur. The clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho. For more information about clearcut please refer to http://bioinformatics.hungry.com/clearcut/

Clearcut is a stand-alone reference implementation of relaxed neighbor joining (RNJ).  

Clearcut is capable of taking either a distance matrix or a multiple sequence alignment (MSA) as input.  If necessary, Clearcut will compute corrected distances based on a configurable distance correction model (Jukes-Cantor or Kimura).  Clearcut outputs a phylogenetic tree in Newick format and an optional corrected distance matrix.    

.. _clearcut_program: http://bioinformatics.hungry.com/clearcut/
.. _clearcut: http://www.mothur.org/wiki/Clearcut

 </help>
</tool>