<tool id="make_rarefaction_plots" name="make_rarefaction_plots" version="1.2.0">
 <description>Generate Rarefaction Plots</description>
 <requirements>
  <requirement type="binary">make_rarefaction_plots.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_datasets='^\S+\.html$:'$plot
  --galaxy_outputdir=$plot.extra_files_path
  make_rarefaction_plots.py
  --input_dir=$input_dir.extra_files_path
  --map_fname=$map_fname
  #if $colorby != None and $colorby.__str__ != 'None' and len($colorby.__str__) > 0:
  --colorby=$colorby
  #end if
  #if $prefs_path != None and $prefs_path.__str__ != 'None':
  --prefs_path=$prefs_path
  #end if
  #if $ymax != None and $ymax.__str__ != '':
  --ymax=$ymax
  #end if
  --background_color=$background_color
  --imagetype=$imagetype
  --resolution=$resolution
  --output_dir=$plot.extra_files_path
 </command>
 <inputs>
  <param name="input_dir" type="data" format="txt" label="input_dir" help="Rarefaction file (I.E. log output from collate_alpha). [REQUIRED]"/>
  <param name="map_fname" type="data" format="tabular" label="map_fname" help="Name of mapping file [REQUIRED]"/>
  <param name="colorby" type="text"  label="colorby" help="Name of columns to make rarefaction graphs of, comma delimited, no spaces. [OPTIONAL]"/>
  <param name="prefs_path" type="data" format="txt" optional="true" label="prefs_path" help="Preferences file for coloring of columns. [OPTIONAL]"/>
  <param name="background_color" type="select" value="white" label="background_color" help="Background color for graphs. [default: white]">
   <option value="white" selected="true">White</option>
   <option value="black">Black</option>
  </param>
  <param name="imagetype" type="select" label="Image Type"
   help="Type of image to produce (i.e. pdf,svg,png). [default: png]">
    <option value="pdf">pdf</option>
    <option value="svg">svg</option>
    <option value="png" selected="true">png</option>
  </param>
  <param name="resolution" type="integer" value="75" label="resolution"
   help="output image resolution, [default: 75]"/>
  <param name="ymax" type="text" label="ymax"
   help="this is the ymax value to be used for the plots, so you can compare rarefaction plots between two different analyses [default: none]"/>
 </inputs>
 <outputs>
  <data format="html" name="plot" label="${tool.name} on ${on_string}"/>
 </outputs>
 <tests>
 </tests>
 <help>This tool takes the log file output from collate_alpha to create an html file of rarefaction plots wherein you can plot by sample and/or by category.
 
For more information, see make_rarefaction_plots_ in the Qiime documentation.
 
Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA

Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN

.. _make_rarefaction_plots: http://qiime.org/scripts/make_rarefaction_plots.html</help>
</tool>