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annotate MetaMA.xml @ 9:328f4031e5d3 draft

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date Wed, 10 May 2017 08:12:48 -0400
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1 <tool id="metaMA" name="Microarray data meta-analysis" version="0.1.0">
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3 <description>Perform meta-analysis thanks to metaMA.</description>
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4
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5 <requirements>
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6 <requirement type="package" version="0.1.0">r-smagexp</requirement>
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7 </requirements>
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8
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9 <stdio>
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10 <exit_code range="1:" />
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11 <regex match="Warning" source="both" level="warning"/>
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12 </stdio>
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14 <command>
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15 <![CDATA[
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16 Rscript
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17 ${__tool_directory__}/MetaMA.R
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18 --input $input
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19 --htmloutput $result_html
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20 --htmloutputpath $result_html.extra_files_path
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21 --htmltemplate ${__tool_directory__}/MetaMa_tpl.html
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22 ]]>
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23 </command>
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25 <inputs>
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26 <param format="rdata" name="input" multiple="true" type="data" optional="false" label="rdata files" help="rdata files containing the results of the analysis to be used in the meta-analysis"/>
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27 </inputs>
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28
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29 <outputs>
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30 <data format="html" name="result_html" label="Meta-analysis results"/>
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31 </outputs>
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32
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33 <help>
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34 <![CDATA[
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35 **What it does**
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37 Given several Rdata object this tool run a meta-analysis using the metaMA R package.
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39 **Results**
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41 - Venn Diagram summarizing the results of the meta-analysis
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42 - A list of indicators to evaluate the quality of the performance of the meta-analysis
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44 - DE : Number of differentially expressed genes
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45 - IDD (Integration Driven discoveries) : number of genes that are declared differentially expressed in the meta-analysis that were not identified in any of the single studies alone
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46 - Loss : Number of genes that are identified differentially expressed in single studies but not in meta-analysis
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47 - DR (Integration-driven Discovery Rate) : corresponding proportion of IDD
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48 - IRR (Integration-driven Revision) : corresponding proportion of Loss
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50 - Fully sortable and requestable table, with gene annotations and hypertext links to NCBI gene database.
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51 ]]>
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52 </help>
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54 </tool>