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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="descriptiveStatistics" name="Descriptive Statistics" version="0.0.16">
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2 <description>Taxonomic and Sample Descriptive 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">descriptiveStatistics.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($OutputFile).strip() != "":
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15 --OutputFile="$OutputFile"
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16 #end if
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17
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18 2&gt;&amp;1</command>
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19 <inputs>
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20 <param optional="false" name="CommunityFile" format="rda" type="data" help="File created by the 'community' function." label="[required] Community File">
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21 <validator type="empty_field" message="This field is required."/>
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22 </param>
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23 <param optional="true" name="Attributes" type="text" help="Comma-separated names of SamplesFile columns on which&#10;descriptive statistics are to be calculated. Example:&#10;Nugent_2_group" size="60" label="Attributes">
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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 </inputs>
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27 <outputs>
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28 <data format="txt" name="OutputFile" label="descriptiveStatistics.txt"/>
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29 </outputs>
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30 <help>
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31 **Description**
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32
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33 Generate descriptive statistics about taxa and samples present in
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34 a CommunityFile.
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35 </help>
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36 </tool>