<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_tmpdir='$__new_file_path__'
  make_rarefaction_plots.py
  --input_dir=$input_dir
  --map_fname=$map_fname
  --colorby=$colorby
  --prefs_path=$prefs_path
  --background_color=$background_color
  --imagetype=$imagetype
  --resolution=$resolution
  --ymax=$ymax
  $webpage
  --output_dir=$__new_file_path__
 </command>
 <inputs>
  <param name="input_dir" type="text"  label="input_dir"
   help="name of folder containing rarefaction files, takes output from collate_alpha.py.  The user can also supply a list of files, which are comma-separated. [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."/>
  <param name="prefs_path" type="text"  label="prefs_path"
   help="preferences file for coloring of columns."/>
  <param name="background_color" type="text" value="white" label="background_color"
   help="Background color for graphs."/>
  <param name="imagetype" type="text" value="png" label="imagetype"
   help="extension for image type choose from (png, svg, pdf).  WARNING: Some formats may not properly open in your browser! [default: png]"/>
  <param name="resolution" type="integer" value="75" label="resolution"
   help="output image resolution, [default: 75]"/>
  <param name="ymax" type="integer" value="-1" 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: ('NO', 'DEFAULT')]"/>
  <param name="webpage" type="boolean" truevalue="" falsevalue="--webpage" checked="false" label="webpage"
   help="this is allows to user to not create the webpage, which may be slow with large datasets [default: True]"/>
 </inputs>
 <outputs>
  
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>