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planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
author bcclaywell
date Mon, 12 Oct 2015 16:46:15 -0400
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1 <tool id="reducedDimensionality" name="Reduced Dimensionality" version="0.0.16">
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2 <description>Taxnomic Dimensionality Reduction (Ordination) Plot</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">reducedDimensionality.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($Attributes).strip() != "":
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12 --Attributes="$Attributes"
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13 #end if
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14 #if str($OrdinationAlgorithm).strip() != "":
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15 --OrdinationAlgorithm="$OrdinationAlgorithm"
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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="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">
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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="OrdinationAlgorithm" type="select" value="MDS" help="Algorithm to use for oridination &quot;PCoA&quot; (Principle&#10;Coordinates Analysis), &quot;NMDS&quot; (Non-Metric Multidimensional&#10;Scaling), &quot;CA&quot; (Correspondence Analysis), &quot;DPCoA&quot; (Double&#10;Principle Components Analysis)." label="Ordination Algorithm" force_select="FALSE">
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30 <validator type="empty_field" message="This field is required."/>
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31 <option value="MDS">MDS</option>
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32 </param>
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33 </inputs>
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34 <outputs>
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35 <data format="pdf" name="OutputFile" label="reducedDimensionality.pdf"/>
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36 </outputs>
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37 <help>
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38 **Description**
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39
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40 Reduce dimensionality of taxonomic abundance.
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41 </help>
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42 </tool>