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annotate MetaMA.xml @ 17:ef7d98f9eb51 draft

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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit f981b0fd5431199f51e2db8c680eb3d2d1d741b6
author sblanck
date Thu, 14 Dec 2017 04:34:43 -0500
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1 <tool id="metaMA" name="Microarray data meta-analysis" version="1.0.0">
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3 <description>Performs meta-analysis thanks to metaMA.</description>
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5 <requirements>
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6 <requirement type="package">bioconductor-affy</requirement>
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7 <requirement type="package">bioconductor-annaffy</requirement>
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8 <requirement type="package">bioconductor-geoquery</requirement>
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9 <requirement type="package">bioconductor-org.hs.eg.db</requirement>
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10 <requirement type="package">r-venndiagram</requirement>
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11 <requirement type="package">r-metama</requirement>
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12 <requirement type="package">r-optparse</requirement>
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13 </requirements>
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14
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15 <stdio>
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16 <exit_code range="1:" />
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17 <regex match="Warning" source="both" level="warning"/>
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18 </stdio>
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19
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20 <command>
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21 <![CDATA[
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22 Rscript
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23 ${__tool_directory__}/MetaMA.R
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24 --input $input
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25 --htmloutput $result_html
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26 --htmloutputpath $result_html.extra_files_path
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27 --htmltemplate ${__tool_directory__}/MetaMa_tpl.html
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28 ]]>
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29 </command>
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30
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31 <inputs>
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32 <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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33 </inputs>
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34
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35 <outputs>
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36 <data format="html" name="result_html" label="Meta-analysis results"/>
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37 </outputs>
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38
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39 <help>
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40 <![CDATA[
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41 **What it does**
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42
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43 Given several Rdata object this tool run a meta-analysis using the metaMA R package.
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44
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45 **Results**
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46
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47 - Venn Diagram summarizing the results of the meta-analysis
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48 - A list of indicators to evaluate the quality of the performance of the meta-analysis
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49
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50 - DE : Number of differentially expressed genes
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51 - 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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52 - Loss : Number of genes that are identified differentially expressed in single studies but not in meta-analysis
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53 - DR (Integration-driven Discovery Rate) : corresponding proportion of IDD
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54 - IRR (Integration-driven Revision) : corresponding proportion of Loss
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55
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56 - Fully sortable and requestable table, with gene annotations and hypertext links to NCBI gene database.
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57 ]]>
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58 </help>
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60 </tool>