<tool id="cooccurrence" name="Cooccurrence" version="0.0.16">
  <description>Taxonomic Co-occurrence Heatmap</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">cooccurrence.R
       #if str($CommunityFile).strip() != "":
          --CommunityFile="$CommunityFile"
       #end if
       #if str($TaxonQuantile).strip() != "":
          --TaxonQuantile="$TaxonQuantile"
       #end if
       #if str($Transform).strip() != "":
          --Transform="$Transform"
       #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>
    <param optional="true" name="TaxonQuantile" type="float" value="0" help="(Optional, default 0) Numeric value between 0 and 1,&#10;limiting only taxa more frequent than the specified quantile." label="Taxon Quantile">
      <validator type="empty_field" message="This field is required."/>
    </param>
    <param optional="true" name="Transform" type="select" help="(Optional; default 'none') Character string defining how&#10;count data are to be transformed prior to calculation of&#10;co-occurrence. Possible values are 'none', 'log1' (log of 1 +&#10;the observed count, to allow for zeros in the data), 'asinh'&#10;(a log-like transformation that handles zeros more&#10;naturally), 'sqrt' (square root, a transformation commonly&#10;used for count data)." label="Transform" force_select="FALSE">
      <validator type="empty_field" message="This field is required."/>
      <option value="none">none</option>
      <option value="log1">log1</option>
      <option value="asinh">asinh</option>
      <option value="sqrt">sqrt</option>
    </param>
  </inputs>
  <outputs>
    <data format="pdf" name="OutputFile" label="cooccurrence.pdf"/>
  </outputs>
  <help>
**Description**

Taxonomic co-occurrence across samples, displayed as a heatmap.
</help>
</tool>