<tool id='rarefaction' name='Rarefaction' version='1.1'>
  <description>Calculate and plot rarefaction curves</description>
  <requirements>
     <requirement type="binary">@BINARY@</requirement>
     <requirement type="package" version="1.33.2">mothur</requirement>
  </requirements>
  <command interpreter="bash">
   rarefactionCurve.sh $ifile.filetype $input $pctIdent $output
  </command>

  <inputs>
    <conditional name='ifile'>
    <param name='filetype' type='select' label='Input file format' 
           help="Based on the formats used in mothur's rarefaction.single">
      <option value='rabund' selected="true">rabund</option>
      <option value='sabund'>sabund</option>
    </param>
    <when value='rabund'>
    <param name='input' type='data' format='rabund' label='OTU list (rabund or sabund format)'
           help="The rabund output from the 'Map Reads to OTU' tool."/>
    </when>
    <when value='sabund'>
    <param name='input' type='data' format='sabund' label='OTU list (rabund or sabund format)'
           help="File in sabund format used by mothur"/>
    </when>
   </conditional>
    <param name='pctIdent' type='float' value='0.97' label='Minimum identity used in OTU clustering' help='Between 0 - 1.0'/>
  </inputs>

  <outputs>
    <data name='output' format='tabular' label="${tool.name} on ${on_string}:rarefaction" />
  </outputs>

  <help>
===========
Description
===========

Rarefaction calculation based on mothur_'s rarefaction.single command, which will calculate the intra-sample rarefaction curves using a re-sampling without replacement approach.

Rarefaction curves provide a way of comparing the richness observed in different samples. Roughly speaking you get the number of OTUs, on average, that you would have been expected to have observed if you hadn't sampled as many individuals. Although a formula exists to generate a rarefaction curve, mothur uses a randomization procedure. It can also help you to assess your sampling intensity. If a rarefaction curve becomes parallel to the x-axis, you can be reasonably confident that you have done a good job of sampling and can trust the observed level of richness. Otherwise, you need to keep sampling. Rarefaction is actually a better measure of diversity than it is of richness.

-----

----------
Input
----------

OTU list
 rabund or sabund format 

----------
Parameters
----------

Input file format
  rabund (default) or
  sabund

Minimum identity used in OTU clustering
  Used for plot generation

------
Output
------

(A) Tab delimited file containing the resultes of the rarefaction analysis. The first column 'numsampled' indicates the level of sampling intensity, by default this information is provided every 100 individuals. This would typically be plotted on the x-axis. The second column is the average number of OTUs that were observed for that sampling intensity based on the number of iterations, which is 1000 by default. This would represent the data for the y-axis for the corresponding minimum identity (default 0.03, which corresponds to 97%). The columns 'lci' and 'hci' represent the confidence intervals.

.. class:: infomark

Use Galaxy's integrated visualization tool to plot the rarefaction curve. The visualization tool is accessible via the 'Visualize' icon in the extended dataset information area. After having launched the integrated visualization tool select the 'Data Controls' tab. In the 'Data Controls' tab select column 1 (*number sampled*) as 'Data column for X' and use column 2 (*minimum identity*) as 'Data column for Y'.

------

===========
Resources
===========

mothur_

.. _mothur: http://www.mothur.org

**Author**

Patrick D. Schloss (pschloss@umich.edu)

**Wrapper Author**

QFAB Bioinformatics (support@qfab.org)
based on jjohnson mothur_toolsuite wrapper
  </help>
  <tests>
    <test>
        <param name="filetype" value="rabund" />
        <param name="input" value="reads2otus.rabund" />
        <param name="pctIdent" value="0.97" />
        <output name="output" file="rarefaction.tabular" ftype="tabular" lines_diff="10" />
    </test>
  </tests>
</tool>