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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="diversityStatistics" name="Diversity Statistics" version="0.0.16">
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2 <description>Taxonomic Diversity Statistics</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">diversityStatistics.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($OutputFile).strip() != "":
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12 --OutputFile="$OutputFile"
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13 #end if
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14
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15 2&gt;&amp;1</command>
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16 <inputs>
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17 <param optional="false" name="CommunityFile" format="rda" type="data" help="File created by the 'community' function." label="[required] Community File">
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18 <validator type="empty_field" message="This field is required."/>
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19 </param>
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20 </inputs>
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21 <outputs>
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22 <data format="csv" name="OutputFile" label="diversityStatistics.csv"/>
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23 </outputs>
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24 <help>
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25 **Description**
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26
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27 Compute per-sample Shannon, Simpson, Chao1, and ACE summary
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28 statistics of taxonomic diversity. Also report per-sample number
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29 of taxa with non-zero read counts, and total number of reads.
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30 </help>
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31 </tool>