<tool id="plot_adjacency" name="Plot Adjacency Matrix">
  <description></description>
  <command interpreter="python">plot_adjacency.py $node_attr $edges $Adjacency \$INSTALL_RUN_PATH/</command>
  <requirements>
    <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
  </requirements>
  <inputs>
    <param format="tabular" name="node_attr" type="data" label="Node Attribute File"/>
    <param type="sif" name="edges" type = data label="Network File"/>
  </inputs>
  <outputs>
    <data format="html" name="Adjacency" label="Adjacency Matrix"/>
  </outputs>
  <stdio>
    <regex match="Error|error"
     source="stdout"
           level="fatal"
           description="Unknown error"/>
    <regex match="Error|error"
     source="stderr"
           level="fatal"
           description="Unknown error"/>
  </stdio>

  <tests>
    <test>
      <param name="input" value="fa_gc_content_input.fa"/>
      <output name="out_file1" file="fa_gc_content_output.txt"/>
    </test>
  </tests>
  <help>
Plot Adjacency Matrix
----------------------------------------

This tool reads in a network SIF file and it's corresponding node attributes
and plots an interactive adjacency matrix in HMTL format

**1) Node Attributes File **
    This file must be output from Network Attributes Tool of the network
	file being input below.

**2) Network File**

Please input a network SIF file matching the Node Attribute file above
  </help>
</tool>