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annotate MetaMA.xml @ 8:e4e6e583b8d9 draft default tip

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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit ad301f84e16455ca3886e9b56e908180dfd66d4f
author sblanck
date Thu, 26 Jul 2018 08:17:53 -0400
parents 3ce32282f6a4
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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1 <tool id="metaMA" name="Microarray data meta-analysis" version="1.0.0">
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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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 <requirement type="package" version="1.3.3">r-upsetr</requirement>
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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14 </requirements>
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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16 <stdio>
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17 <exit_code range="1:" />
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18 <regex match="Warning" source="both" level="warning"/>
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19 </stdio>
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21 <command>
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22 <![CDATA[
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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23 Rscript
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24 ${__tool_directory__}/MetaMA.R
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25 --input $input
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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26 --species $species
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27 --htmloutput $result_html
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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28 --htmloutputpath $result_html.extra_files_path
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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29 --htmltemplate ${__tool_directory__}/MetaMa_tpl.html
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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30 ]]>
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31 </command>
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33 <inputs>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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34 <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"/>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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35 <param name="species" type="select" optionnal="false" label="species" help="species for annotation">
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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36 <option value="org.Bt.eg.db">Bovine</option>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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37 <option value="org.Cf.eg.db">Canine</option>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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38 <option value="org.Gg.eg.db">Chicken</option>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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39 <option value="org.Dm.eg.db">Fly</option>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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40 <option value="org.Hs.eg.db">Human</option>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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41 <option value="org.Mm.eg.db">Mouse</option>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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42 <option value="org.Ss.eg.db">Pig</option>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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43 <option value="org.Rn.eg.db">Rat</option>
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44 <option value="org.Ce.eg.db">Worm</option>
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45 <option value="org.Dr.eg.db">Zebrafish</option>
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46 </param>
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47 </inputs>
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49 <outputs>
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50 <data format="html" name="result_html" label="Meta-analysis results"/>
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51 </outputs>
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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53 <help>
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54 <![CDATA[
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55 **What it does**
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57 Given several Rdata object this tool run a meta-analysis using the metaMA R package.
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58
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59 **Results**
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60
6
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61 - Venn Diagram or upsetR diagram (when the number of studies is greater than 2) summarizing the results of the meta-analysis
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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62 - A list of indicators to evaluate the quality of the performance of the meta-analysis
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64 - DE : Number of differentially expressed genes
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65 - 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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66 - Loss : Number of genes that are identified differentially expressed in single studies but not in meta-analysis
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67 - DR (Integration-driven Discovery Rate) : corresponding proportion of IDD
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68 - IRR (Integration-driven Revision) : corresponding proportion of Loss
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70 - Fully sortable and requestable table, with gene annotations and hypertext links to NCBI gene database.
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71 ]]>
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72 </help>
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74 </tool>