<tool id="presenceAbsence" name="Presence Absence" version="0.0.16">
  <description>Taxonomic Presence / Absence Summary and Chi-squared Test</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">presenceAbsence.R
       #if str($CommunityFile).strip() != "":
          --CommunityFile="$CommunityFile"
       #end if
       #if str($Attribute).strip() != "":
          --Attribute="$Attribute"
       #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="Attribute" type="text" help="Name of a sample attribute to summarize presence / absence&#10;data. Example: Nugent_2_group" size="60" label="Attribute">
      <validator type="empty_field" message="This field is required."/>
    </param>
  </inputs>
  <outputs>
    <data format="csv" name="OutputFile" label="presenceAbsence.csv"/>
  </outputs>
  <help>
**Description**

Summarize samples with each taxon present, grouped by factor
</help>
</tool>