--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime/make_rarefaction_plots.xml	Wed Jun 06 16:40:30 2012 -0400
@@ -0,0 +1,62 @@
+<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>
+