--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make_rarefaction_plots.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,50 @@
+<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>
+