<tool id="plot_taxa_summary" name="plot_taxa_summary" version="2.0.0">
 <description>Make taxaonomy summary charts based on taxonomy assignment</description>
 <requirements>
  <requirement type="binary">plot_taxa_summary.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_outputdir='$taxonomy_summary_chart.extra_files_path'
  --galaxy_datasets='^\S+_charts\.html$:'$taxonomy_summary_chart
  plot_taxa_summary.py
  #set $counts = []
  #for i in $inputs:
    #set $counts = $counts + [$i.counts_fname.__str__]
  #end for
  --counts_fname=#echo ','.join($counts)
  #if $labels != None and $labels.__str__ != 'None' and $labels.__str__ != '':
  --labels=$labels
  #end if
  --num_categories=$num_categories
  #if $colorby != None and $colorby.__str__ != 'None' and $colorby.__str__ != '':
  --colorby=$colorby
  #end if
  #if $prefs_path != None and $prefs_path.__str__ != 'None':
  --prefs_path=$prefs_path
  #end if
  --background_color=$background_color
  --dpi=$dpi
  --x_width=$x_width
  --y_height=$y_height
  --bar_width=$bar_width
  --type_of_file=$type_of_file
  --chart_type=$chart_type
  --resize_nth_label=$resize_nth_label
  $include_html_legend
  $include_html_counts
  --label_type=$label_type
  --dir_path='$taxonomy_summary_chart.extra_files_path'
 </command>
 <inputs>
  <repeat name="inputs" title="Taxa Summary">
    <param name="counts_fname" type="data" format="txt" label="counts_fname"
     help="Summarized taxa file [REQUIRED]"/>
  </repeat>
  <param name="labels" type="text"  label="labels"
   help="list of labels (i.e. Phylum, Class) [REQUIRED]"/>
  <param name="num_categories" type="text" value="20" label="num_categories"
   help="Maximum number of individual categories in each pie chart. All additional categories are grouped into an 'other' category. NOTE: this is only used for the pie charts. [default: 20]"/>
  <param name="colorby" type="text"  label="colorby"
   help="This is the samples to make charts for in the counts files from summarize_taxa.py. The sample name must match the name of a sample id in the header of the counts file exactly and multiple categories can be list by comma separating them without spaces.  [default: None]"/>
  <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. The label taxonomy_coloring is used for the coloring, see example prefs file preferences_file. [default: None]"/>
  <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="dpi" type="text" value="80" label="dpi"
   help="This is the dpi to use in the plots. [default: 80]"/>
  <param name="x_width" type="text" value="12" label="x_width"
   help="This is the width to use in the plots. [default: 12]"/>
  <param name="y_height" type="text" value="6" label="y_height"
   help="This is the height to use in the plots. [default: 6]"/>
  <param name="bar_width" type="text" value="0.75" label="bar_width"
   help="This the width of the bars in the bar graph and should be a number between 0 and 1. NOTE: this is only used for bar charts. [default: 0.75]"/>
  <param name="type_of_file" type="select" label="type_of_file"
   help="This is the filename suffix to use for each high-res plot. (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="chart_type" type="select" label="chart_type"
   help="type of chart to plot (i.e. pie, bar or area). [default: area]">
   <option value="area" selected="true">Area</option>
   <option value="bar">Bar</option>
   <option value="pie">Pie</option>
   </param>
  <param name="resize_nth_label" type="text" value="0" label="resize_nth_label"
   help="this is for large area and bar charts where the font on the x-axis is small. This allows you to set every nth label to be larger on the x-axis.This requires an integer value greater than 0.[default: 0]"/>
  <param name="include_html_legend" type="boolean" truevalue="--include_html_legend" falsevalue="" checked="false" label="include_html_legend" help="Include HTML legend. If present, the writing of the legend in the html page is included. [default: False]"/>
  <param name="include_html_counts" type="boolean" truevalue="--include_html_counts" falsevalue="" checked="false" label="include_html_counts" help="Include HTML counts. If present, the writing of the counts in the html table is included [default: False]"/>
  <param name="label_type" type="select" label="label_type" help="Label type. If the label type is numeric, the x-axis will be scaled accordingly. Otherwise, the values will be evenly-spaced and treated categorically. [Default: categorical]">
   <option value="categorical" selected="true">Categorical</option>
   <option value="numerical">Numerical</option>
   </param>
 </inputs>
 <outputs>
  <data name="taxonomy_summary_chart" format="html" label="${tool.name} on ${on_string}: taxonomy_summary_chart: $chart_type"/>
 </outputs>
 <tests>
 </tests>
 <help>For more information, see plot_taxa_summary_ in the Qiime documentation.
 
Updated and validated 01/20/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA

Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
 
 .. _plot_taxa_summary: http://qiime.org/scripts/plot_taxa_summary.html</help>
</tool>