<tool id="categorized_dist_scatterplot" name="categorized_dist_scatterplot" version="1.2.1">
 <description>makes a figure representing average distances between samples, broken down by categories. I call it a 'categorized distance scatterplot'</description>
 <requirements>
  <requirement type="binary">categorized_dist_scatterplot.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_tmpdir='$__new_file_path__'
  categorized_dist_scatterplot.py
  --map=$map
  --distance_matrix=$distance_matrix
  --primary_state=$primary_state
  --axis_category=$axis_category
  --output_path=$output_path
  --colorby=$colorby
  --secondary_state=$secondary_state
 </command>
 <inputs>
  <param name="map" type="data" format="tabular" label="map"
   help="mapping file [REQUIRED]"/>
  <param name="distance_matrix" type="text"  label="distance_matrix"
   help="distance matrix [REQUIRED]"/>
  <param name="primary_state" type="text"  label="primary_state"
   help="Samples matching this state will be plotted. E.g.: AgeCategory:Child . See qiime's filter_by_metadata.py for more syntax options [REQUIRED]"/>
  <param name="axis_category" type="text"  label="axis_category"
   help="this will form the horizontal axis of the figure, e.g.: AgeYears . Must be numbers [REQUIRED]"/>
  <param name="colorby" type="text"  label="colorby"
   help="samples will first be separated by this column of the mapping file. They will be colored by this column of the mapping file, and all comparisons will be done only among samples with the same value in this column. e.g.: Country. You may omit -c, and the samples will not be separated"/>
  <param name="secondary_state" type="text"  label="secondary_state"
   help="all samples matching the primary state will be compared to samples matcthing this secondary state. E.g.: AgeCategory:Adult"/>
 </inputs>
 <outputs>
  <data format="txt" name="output_path"/>
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>