<tool id="make_2d_plots" name="make_2d_plots" version="2.0.0">
 <description>Make 2D PCoA Plots</description>
 <requirements>
  <requirement type="binary">make_2d_plots.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_outputdir=$plot.extra_files_path
  ##--galaxy_tmpdir='$__new_file_path__'
  ##--galaxy_datasets='^\S+_2D_PCoA_plots\.html$:'$plot
  --galaxy_datasets='^\S+\.html$:'$plot
  ##--galaxy_datasetid=$output1.id
  ##--galaxy_new_files_path='$__new_file_path__'
  ##--galaxy_tmpdir='$__new_file_path__'
  make_2d_plots.py
  --coord_fname=$coord_fname
  --map_fname=$map_fname
  #if $colorby != None and $colorby.__str__ != 'None':
  --colorby=$colorby
  #end if
  #if $prefs_path != None and $prefs_path.__str__ != 'None' and len($prefs_path.__str__) > 0:
  --prefs_path=$prefs_path
  #end if
  --background_color=$background_color
  --ellipsoid_opacity=$ellipsoid_opacity
  --ellipsoid_method=$ellipsoid_method
  #if $master_pcoa != None and $master_pcoa.__str__ != 'None' and len($master_pcoa.__str__) > 0:
  --master_pcoa=$master_pcoa
  #end if
  --output_dir=$plot.extra_files_path
 </command>
 <inputs>
  <param name="coord_fname" type="data" format="qiimepca" label="coord_fname"
   help="This is the path to the principal coordinates file (i.e., resulting file from principal_coordinates.py).  Alternatively, the user can supply a directory containing multiple principal coordinates files. [REQUIRED]"/>
  <param name="map_fname" type="data" format="tabular" label="map_fname"
   help="This is the metadata mapping file [REQUIRED]"/>
  <param name="colorby" type="text"  label="colorby"
   help="This is the categories to color by in the plots from the user-generated mapping file. The categories must match the name of a column header in the mapping file exactly and multiple categories can be list by comma separating them without spaces. The user can also combine columns in the mapping file by separating the categories by '&#38;&#38;' without spaces [default=color by all; leave blank]"/>
  <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 [OPTIONAL]"/>
  <param name="background_color" type="text"  label="background_color"
   help="This is the background color to use in the plots. [default: white]" value="white"/>
  <param name="ellipsoid_opacity" type="float" value="0.33" label="ellipsoid_opacity"
   help="Used when plotting ellipsoids for jackknifed beta diversity (i.e. using a directory of coord files instead of a single coordfile). Valid range is 0-1. A value of 0 produces completely transparent (invisible) ellipsoids. A value of 1 produces completely opaque ellipsoids. [default=0.33]"/>
  <param name="ellipsoid_method" type="select" value="IQR" label="ellipsoid_method"
   help="Used when plotting ellipsoids for jackknifed beta diversity (i.e. using a directory of coord files instead of a single coord file). Choose between 'IQR' (The Interquartile Range) and 'sdev' (The standard deviation). [default=IQR]">
    <option value="IQR" selected="true">IQR</option>
    <option value="sdev">sdev</option>
   </param>
  <param name="master_pcoa" type="text"  label="master_pcoa"
   help="Used only when plotting ellipsoids for jackknifed beta diversity (i.e. using a directory of coord files instead of a single coord file). These coordinates will be the center of each ellipisoid. [default: None; arbitrarily chosen PC matrix will define the center point]"/>
 </inputs>
 <outputs>
 <data format="html" name="plot" label="${tool.name} on ${on_string}"/>
 </outputs>
 <tests>
 </tests>
 <help>For more information, see make_2d_plots_ 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_2d_plots: http://qiime.org/scripts/make_2d_plots.html</help>
</tool>