<tool id="diversityStatistics" name="Diversity Statistics" version="0.0.16">
  <description>Taxonomic Diversity Statistics</description>
  <requirements>
    <requirement type="package" version="3.1.2">R</requirement>
    <requirement type="package" version="2014-05-02">microbiome_community</requirement>
  </requirements>
  <command interpreter="Rscript --vanilla">diversityStatistics.R
       #if str($CommunityFile).strip() != "":
          --CommunityFile="$CommunityFile"
       #end if
       #if str($OutputFile).strip() != "":
          --OutputFile="$OutputFile"
       #end if

2&gt;&amp;1</command>
  <inputs>
    <param optional="false" name="CommunityFile" format="rda" type="data" help="File created by the 'community' function." label="[required] Community File">
      <validator type="empty_field" message="This field is required."/>
    </param>
  </inputs>
  <outputs>
    <data format="csv" name="OutputFile" label="diversityStatistics.csv"/>
  </outputs>
  <help>
**Description**

Compute per-sample Shannon, Simpson, Chao1, and ACE summary
statistics of taxonomic diversity. Also report per-sample number
of taxa with non-zero read counts, and total number of reads.
</help>
</tool>