--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime/make_prefs_file.xml	Wed Jun 06 16:40:30 2012 -0400
@@ -0,0 +1,54 @@
+<tool id="make_prefs_file" name="make_prefs_file" version="2.0.0">
+ <description>Generate preferences file</description>
+ <requirements>
+  <requirement type="binary">make_prefs_file.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  make_prefs_file.py
+  --map_fname=$map_fname
+  --output_fp=$output_fp
+  #if $mapping_headers_to_use != None and $mapping_headers_to_use.__str__ != '':
+  --mapping_headers_to_use=$mapping_headers_to_use
+  #end if
+  --background_color=$background_color
+  --monte_carlo_dists=$monte_carlo_dists
+  #if $input_taxa_file != None and $input_taxa_file.__str__ != '' and $input_taxa_file.__str__ != 'None':
+  --input_taxa_file=$input_taxa_file
+  #end if
+  --ball_scale=$ball_scale
+  --arrow_line_color=$arrow_line_color
+  --arrow_head_color=$arrow_head_color
+ </command>
+ <inputs>
+  <param name="map_fname" type="data" format="tabular" label="map_fname"
+   help="This is the metadata mapping file [REQUIRED]"/>
+  <param name="mapping_headers_to_use" type="text" label="mapping_headers_to_use"
+   help="mapping fields to use in prefs file [default: leave empty; ALL]"/>
+  <param name="background_color" type="text" value="black" label="background_color"
+   help="This is the background color to  use in the plots. [default: black]"/>
+  <param name="monte_carlo_dists" type="text" value="10" label="monte_carlo_dists"
+   help="monte carlo distanceto use for each sample header [default: 10]"/>
+  <param name="input_taxa_file" type="data" format="txt" optional="true" label="input_taxa_file"
+   help="summarized taxa file with samplecounts by taxonomy (resulting file from summarize_taxa.py)"/>
+  <param name="ball_scale" type="float" value="1.0" label="ball_scale"
+   help="scale factor for the size of each ball in the plots [default: 1.0]"/>
+  <param name="arrow_line_color" type="text" value="white" label="arrow_line_color"
+   help="arrow line color forprocrustes analysis. [default: white]"/>
+  <param name="arrow_head_color" type="text" value="red" label="arrow_head_color"
+   help="arrow head color forprocrustes analysis. [default: red]"/>
+ </inputs>
+ <outputs>
+  <data format="txt" name="output_fp"/>
+ </outputs>
+ <tests>
+ </tests>
+ <help>For more information, see make_prefs_file_ in the Qiime documentation.
+ 
+Updated and validated 01/18/12 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_prefs_file: http://qiime.org/scripts/make_prefs_file.html</help>
+</tool>
+