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annotate cooccurrence.xml @ 0:12b4f093e6c4 draft default tip

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author bcclaywell
date Mon, 12 Oct 2015 16:46:15 -0400
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1 <tool id="cooccurrence" name="Cooccurrence" version="0.0.16">
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2 <description>Taxonomic Co-occurrence Heatmap</description>
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3 <requirements>
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4 <requirement type="package" version="3.1.2">R</requirement>
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5 <requirement type="package" version="2014-05-02">microbiome_community</requirement>
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6 </requirements>
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7 <command interpreter="Rscript --vanilla">cooccurrence.R
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8 #if str($CommunityFile).strip() != "":
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9 --CommunityFile="$CommunityFile"
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10 #end if
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11 #if str($TaxonQuantile).strip() != "":
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12 --TaxonQuantile="$TaxonQuantile"
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13 #end if
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14 #if str($Transform).strip() != "":
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15 --Transform="$Transform"
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16 #end if
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17 #if str($OutputFile).strip() != "":
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18 --OutputFile="$OutputFile"
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19 #end if
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20
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21 2&gt;&amp;1</command>
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22 <inputs>
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23 <param optional="false" name="CommunityFile" format="rda" type="data" help="File created by the 'community' function." label="[required] Community File">
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24 <validator type="empty_field" message="This field is required."/>
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25 </param>
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26 <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">
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27 <validator type="empty_field" message="This field is required."/>
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28 </param>
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29 <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">
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30 <validator type="empty_field" message="This field is required."/>
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31 <option value="none">none</option>
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32 <option value="log1">log1</option>
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33 <option value="asinh">asinh</option>
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34 <option value="sqrt">sqrt</option>
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35 </param>
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36 </inputs>
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37 <outputs>
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38 <data format="pdf" name="OutputFile" label="cooccurrence.pdf"/>
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39 </outputs>
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40 <help>
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41 **Description**
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42
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43 Taxonomic co-occurrence across samples, displayed as a heatmap.
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44 </help>
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45 </tool>