<tool id="make_3d_plots" name="make_3d_plots" version="1.2.1">
 <description>Make 3D PCoA plots</description>
 <requirements>
  <requirement type="binary">make_3d_plots.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_summary_html='$output_html'
  --galaxy_outputdir='$output_html.extra_files_path'
  --galaxy_summary_template='$output_template'
  make_3d_plots.py
  --coord_fname=$coord_fname
  --map_fname=$map_fname
  --colorby=$colorby
  --custom_axes=$custom_axes
  --prefs_path=$prefs_path
  --background_color=$background_color
  --output_dir=$__new_file_path__
  --ellipsoid_smoothness=$ellipsoid_smoothness
  --ellipsoid_opacity=$ellipsoid_opacity
  --ellipsoid_method=$ellipsoid_method
  --taxa_fname=$taxa_fname
  --n_taxa_keep=$n_taxa_keep
  --biplot_output_file=$biplot_output_file
  --master_pcoa=$master_pcoa
  --output_format=$output_format
  --interpolation_points=$interpolation_points
  --polyhedron_points=$polyhedron_points
  --polyhedron_offset=$polyhedron_offset
 </command>
 <inputs>
  <param name="coord_fname" type="text"  label="coord_fname"
   help="This is the path to the principal coordinates file (i.e., resulting file from principal_coordinates.py), or to a directory containing multiple coord files for averaging (e.g. resulting files from multiple_rarefactions_even_depth.py, followed by multiple beta_diversity.py, followed by multiple principal_coordinates.py). [REQUIRED]"/>
  <param name="map_fname" type="data" format="tabular" label="map_fname"
   help="This is the metadata mapping file  [default=('NO', 'DEFAULT')] [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=('NO', 'DEFAULT')]"/>
  <param name="custom_axes" type="text"  label="custom_axes"
   help="This is the category from the user-generated mapping file to use as a custom axis in the plot.  For instance,there is a pH category and would like to seethe samples plotted on that axis instead of PC1, PC2, etc., one can use this option.  It is also useful for plotting time-series data [default: ('NO', 'DEFAULT')]"/>
  <param name="prefs_path" type="text"  label="prefs_path"
   help="This is the user-generated preferences file. NOTE: This is a file with a dictionary containing preferences for the analysis [default: ('NO', 'DEFAULT')]"/>
  <param name="background_color" type="text"  label="background_color"
   help="This is the background color to use in the plots (Options are 'black' or 'white'. [default: ('NO', 'DEFAULT')]"/>
  <param name="ellipsoid_smoothness" type="text" value="1" label="ellipsoid_smoothness"
   help="The level of smoothness used in plotting ellipsoids for a summary plot (i.e. using a directory of coord files instead of a single coord file). Valid range is 0-3. A value of 0 produces very coarse 'ellipsoids' but is fast to render. The default value is 2. If you encounter a memory error when generating or displaying the plots, try including just one metadata column in your plot. If you still have trouble, reduce the smoothness level to 0 or 1."/>
  <param name="ellipsoid_opacity" type="text" value="0.33" label="ellipsoid_opacity"
   help="Used when plotting ellipsoids for a summary plot (i.e. using a directory of coord files instead of a single coord file). Valid range is 0-3. A value of 0 produces completely transparent (invisible) ellipsoids. A value of 1 produces completely opaque ellipsoids. The default value is 0.33."/>
  <param name="ellipsoid_method" type="text" value="IQR" label="ellipsoid_method"
   help="Used when plotting ellipsoids for a summary plot (i.e. using a directory of coord files instead of a single coord file). Valid values are 'IQR' (The Interquartile Range) and 'sdev' (The standard deviation). The default is IQR."/>
  <param name="taxa_fname" type="text"  label="taxa_fname"
   help="If you wish to perform a biplot, where taxa are plotted along with samples, supply an otu table format file.  Typically this is the output from summarize_taxa.py."/>
  <param name="n_taxa_keep" type="text" value="10" label="n_taxa_keep"
   help="If performing a biplot, the number of taxa to display; use -1 to display all. [default: 10]"/>
  <param name="biplot_output_file" type="data" format="txt" label="biplot_output_file"
   help="If performing a biplot, save the biplot coordinates in this file. [default: %default]"/>
  <param name="master_pcoa" type="text"  label="master_pcoa"
   help="If performing averaging on multiple coord files, the other coord files will be aligned to this one through procrustes analysis. This master file will not be included in the averaging. If this master coord file is not provided, one of the other coord files will be chosen arbitrarily as the target alignment. [default: %default]"/>
  <param name="interpolation_points" type="integer" value="0" label="interpolation_points"
   help="Number of extra points to use between samples and interpolate, the minimum is 2. Only used with the inVUE output. [default: 0]"/>
  <param name="polyhedron_points" type="integer" value="4" label="polyhedron_points"
   help="Points to be generated  to create a frame around the PCoA plots. Only used when --output_format is  inVUE. [default: 4]"/>
  <param name="polyhedron_offset" type="float" value="1.5" label="polyhedron_offset"
   help="Offset to be added to  the points created in the --polyheadron_points option. Only used when  --output_format is inVUE. [default: 1.5]"/>
  <param name="output_format"type="select" label="output_format">
   <option value="king" selected="true">king</option>
   <option value="invue">invue</option>
  </param>
 </inputs>
 <configfiles>
  <configfile name="output_template">
<![CDATA[
<html>
<body>
<a href="rarefaction_plots.html">weighted_unifrac_pc.txt_3D.html</a>
</body>
</html>
]]>
  </configfile>
 </configfiles>
 <outputs>
  <data format="html" name="output_html" label="alpha_rarefaction_plots"/>
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>