view mothur/tools/mothur/sens.spec.xml @ 2:e990ac8a0f58

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

<tool id="mothur_sens_spec" name="Sens.spec" version="1.19.0" >
 <description>Determine the quality of OTU assignment</description>
 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  --cmd='sens.spec'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sensspec$:'$sensspec
  --outputdir='$logfile.extra_files_path'
  --list=$list
  #if isinstance($dist.datatype, $__app__.datatypes_registry.get_datatype_by_extension('pair.dist').__class__):
   --column=$dist
  #else
   --phylip=$dist
  #end if
  #if $label.__str__ != "None" and len($label.__str__) > 0:
   --label='$label'
  #end if
  #if len($precision.__str__) > 0:
   --precision=$precision
  #end if
  #if float($cutoff.__str__) > 0.0:
   --cutoff=$cutoff
  #end if
  $hard
 </command>
 <inputs>
  <param name="list" type="data" format="list" label="list - OTU List"/>
  <param name="dist" type="data" format="dist" label="phylip,column - Distance Matrix"/>
  <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" 
     help="By default all are included if no selection is made.">
   <options from_dataset="list">
    <column name="name" index="0"/>
    <column name="value" index="0"/>
   </options>
  </param>
  <param name="precision" type="integer" value="100" optional="true" label="precision - Precision for rounding distance values"/>
  <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" 
                 help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
  <param name="hard" type="boolean" checked="false" truevalue="--hard=true" falsevalue="" label="hard - Use hard cutoff instead of rounding"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="sensspec" label="${tool.name} on ${on_string}: sensspec" />
 </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 sens.spec_ command takes a list_ and either a column_  or phylip_ distance matrix to determine the quality of OTU assignment.


.. _list: http://www.mothur.org/wiki/List_file
.. _column: http://www.mothur.org/wiki/Column-formatted_distance_matrix
.. _phylip: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
.. _sens.spec: http://www.mothur.org/wiki/Sens.spec

 </help>
</tool>