<tool id="make_distance_histograms" name="make_distance_histograms" version="2.0.0">
 <description>Make distance histograms</description>
 <requirements>
  <requirement type="binary">make_distance_histograms.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_outputdir=$plot.extra_files_path
  --galaxy_datasets='^\S+\.html$:'$plot
  make_distance_histograms.py
  --distance_matrix_file=$distance_matrix_file
  --map_fname=$map_fname
  #if $prefs_path != None and $prefs_path.__str__ != 'None' and len($prefs_path.__str__) > 0:
  --prefs_path=$prefs_path
  #end if
  --dir_path=$plot.extra_files_path
  --background_color=$background_color
  $monte_carlo
  #if $fields != None and $fields.__str__ != ' ' and $fields.__str__ !='':
  --fields=$fields
  #end if
  --monte_carlo_iters=$monte_carlo_iters
 </command>
 <inputs>
  <param name="distance_matrix_file" type="data" format="qiimedistmat" label="distance_matrix_file"
   help="Path to distance matrix file (IE, the output from beta diversity). [REQUIRED]"/>
  <param name="map_fname" type="data" format="tabular" label="map_fname"
   help="This is the metadata mapping file [REQUIRED]"/>
  <param name="prefs_path" type="data" format="txt"  optional="true" label="prefs_path"
   help="This is the user-generated preferences file. NOTE: This is a file with a dictionary containing preferences for the analysis.  This dict must have a 'Fields' key mapping to a list of desired fields. [default: ('NO', 'DEFAULT')]"/>
  <param name="background_color" type="select" label="background_color"
   help="This is the background color to use in the plots [default: white]">
    <option value="white" selected="true">White</option>
    <option value="black">Black</option>
    </param>
  <param name="monte_carlo" type="boolean" truevalue="--monte_carlo" falsevalue="" checked="false" label="monte_carlo"
   help="Perform Monte Carlo analysis on distances.  [Default: False]"/>
  <param name="fields" type="text"  label="fields"
   help="Comma delimited list of fields to compare. Put list of fields in quotes. This overwrites fields in prefs file. If this is not provided, the first field in metadata mapping file will be used.  Usage: 'Field1,Field2,Field3'"/>
  <param name="monte_carlo_iters" type="integer" value="0" label="monte_carlo_iters"
   help="Number of iterations to perform for Monte Carlo analysis. [default: 0/no monte carlo simulation performed]"/>
 </inputs>
 <outputs>
 <data format="html" name="plot" label="${tool.name} on ${on_string}"/>
 </outputs>
 <tests>
 </tests>
 <help>For more information, see make_distance_histograms_ 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_distance_histograms: http://qiime.org/scripts/make_distance_histograms.html</help>
</tool>