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

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

<tool id="mothur_nmds" name="Nmds" version="1.19.0">
 <description>generate non-metric multidimensional scaling data</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='nmds'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.nmds\.axes$:'$nmds_axes,'^\S+\.nmds\.iters$:'$nmds_iters,'^\S+\.nmds\.stress$:'$stress_nmds
  --outputdir='$logfile.extra_files_path'
  --phylip=$dist
  #if $axes.__str__ != "None" and len($axes.__str__) > 0:
   --axes=$axes
  #end if
  #if int($mindim.__str__) > 0:
   --mindim=$mindim
  #end if
  #if int($maxdim.__str__) >= int($mindim.__str__):
   --maxdim=$maxdim
  #end if
  #if int($iters.__str__) > 0:
   --iters=$iters
  #end if
  #if int($maxiters.__str__) > 0:
   --maxiters=$maxiters
  #end if
  #if float($epsilon.__str__) > 0.0:
   --epsilon=$epsilon
  #end if
 </command>
 <inputs>
  <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
  <param name="axes" type="data" format="axes" optional="true" label="axes - a starting configuration"/>
  <param name="mindim" type="integer" value="2" label="mindim - minimum dimensions (default 2)"/>
  <param name="maxdim" type="integer" value="2" label="maxdim - maximum dimensions (default 2)"/>
  <param name="iters" type="integer" value="10" label="iters - Number of random configuration to try (default 10)"/>
  <param name="maxiters" type="integer" value="500" label="maxiters - Number of iterations to try with each random configuration (default 500)"/>
  <param name="epsilon" type="float" optional="true" value="1e-12" label="epsilon - acceptable stopping precision (default 1e-12)"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="axes" name="nmds_axes" label="${tool.name} on ${on_string}: nmds.axes"/>
  <data format="tabular" name="nmds_iters" label="${tool.name} on ${on_string}: nmds.iters"/>
  <data format="tabular" name="stress_nmds" label="${tool.name} on ${on_string}: nmds.stress"/>
 </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 nmds_ command generates non-metric multidimensional scaling data from a phylip_distance_matrix_.

.. _phylip_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
.. _nmds: http://www.mothur.org/wiki/Nmds


 </help>
</tool>