<tool id="ribbonPlot" name="Ribbon Plot" version="0.0.16">
  <description>Attribute Ribbon Plot of Clustered Samples</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">ribbonPlot.R
       #if str($CommunityFile).strip() != "":
          --CommunityFile="$CommunityFile"
       #end if
       #if str($Attributes).strip() != "":
          --Attributes="$Attributes"
       #end if
       #if str($ClusteringAlgorithm).strip() != "":
          --ClusteringAlgorithm="$ClusteringAlgorithm"
       #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="Attributes" type="text" help="Comma-separated names of SamplesFile columns on which&#10;ribbons are to be plotted. Samples are ordered by the first&#10;element of Attributes; Attributes must identify more than 1&#10;SampleFile column. Example: Nugent_3_group, Amsel,&#10;Nugent_Lactobacillus, pH, Clue" size="60" label="Attributes">
      <validator type="empty_field" message="This field is required."/>
    </param>
    <param optional="true" name="ClusteringAlgorithm" type="select" help="Algorithm to use for clustering samples, one of&#10;&quot;hclust&quot; or 'DirichletMultinomial&quot; (from the&#10;DirichletMultinomial package)." label="Clustering Algorithm" force_select="FALSE">
      <validator type="empty_field" message="This field is required."/>
      <option value="hclust">hclust</option>
      <option value="DirichletMultinomial">DirichletMultinomial</option>
    </param>
  </inputs>
  <outputs>
    <data format="svg" name="OutputFile" label="ribbonPlot.svg"/>
  </outputs>
  <help>
**Description**

Attributes of samples as heat maps, with samples clustered by one
of several algorithms
</help>
</tool>