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comparison diversityStatistics.xml @ 0:12b4f093e6c4 draft default tip

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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">
2 <description>Taxonomic Diversity Statistics</description>
3 <requirements>
4 <requirement type="package" version="3.1.2">R</requirement>
5 <requirement type="package" version="2014-05-02">microbiome_community</requirement>
6 </requirements>
7 <command interpreter="Rscript --vanilla">diversityStatistics.R
8 #if str($CommunityFile).strip() != "":
9 --CommunityFile="$CommunityFile"
10 #end if
11 #if str($OutputFile).strip() != "":
12 --OutputFile="$OutputFile"
13 #end if
14
15 2&gt;&amp;1</command>
16 <inputs>
17 <param optional="false" name="CommunityFile" format="rda" type="data" help="File created by the 'community' function." label="[required] Community File">
18 <validator type="empty_field" message="This field is required."/>
19 </param>
20 </inputs>
21 <outputs>
22 <data format="csv" name="OutputFile" label="diversityStatistics.csv"/>
23 </outputs>
24 <help>
25 **Description**
26
27 Compute per-sample Shannon, Simpson, Chao1, and ACE summary
28 statistics of taxonomic diversity. Also report per-sample number
29 of taxa with non-zero read counts, and total number of reads.
30 </help>
31 </tool>