<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>