comparison mothur/tools/mothur/clearcut.xml @ 35:95d75b35e4d2

Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)

34:1be61ceb20d7

<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":

  <data format="lower.dist" name="matrix" label="${tool.name} on ${on_string}: Phylip Distance Matrix" >
   <filter>matrixout == True</filter>
  </data>
 </outputs>
 <requirements>
  <requirement type="package" version="1.27">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**

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>

35:95d75b35e4d2

<tool id="mothur_clearcut" name="Clearcut" version="1.20.0">
 <description>Generate a tree using relaxed neighbor joining</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='clearcut'
  #if $matrixout == True or $matrixout.__str__ == "true":

  <data format="lower.dist" name="matrix" label="${tool.name} on ${on_string}: Phylip Distance Matrix" >
   <filter>matrixout == True</filter>
  </data>
 </outputs>
 <requirements>
  <requirement type="package" version="1.33">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**

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

v.1.20.0: Trivial upgrade to Mothur 1.33

 </help>
</tool>