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annotate MetaMA.xml @ 39:07ac07715f22 draft default tip
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 7026b0fbe3611962c37c7f9b5f001434f059e32c
| author | sblanck |
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| date | Tue, 26 Jun 2018 04:14:25 -0400 |
| parents | 22e1325aaa88 |
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| rev | line source |
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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160-dirty
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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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4 |
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5 <requirements> |
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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit f981b0fd5431199f51e2db8c680eb3d2d1d741b6
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6 <requirement type="package">bioconductor-affy</requirement> |
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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit f981b0fd5431199f51e2db8c680eb3d2d1d741b6
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7 <requirement type="package">bioconductor-annaffy</requirement> |
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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit f981b0fd5431199f51e2db8c680eb3d2d1d741b6
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8 <requirement type="package">bioconductor-geoquery</requirement> |
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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit f981b0fd5431199f51e2db8c680eb3d2d1d741b6
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9 <requirement type="package">bioconductor-org.hs.eg.db</requirement> |
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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit f981b0fd5431199f51e2db8c680eb3d2d1d741b6
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10 <requirement type="package">r-venndiagram</requirement> |
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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit f981b0fd5431199f51e2db8c680eb3d2d1d741b6
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11 <requirement type="package">r-metama</requirement> |
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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit f981b0fd5431199f51e2db8c680eb3d2d1d741b6
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12 <requirement type="package">r-optparse</requirement> |
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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00
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13 <requirement type="package" version="1.3.3">r-upsetr</requirement> |
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14 </requirements> |
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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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20 |
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21 <command> |
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22 <![CDATA[ |
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23 Rscript |
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24 ${__tool_directory__}/MetaMA.R |
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25 --input $input |
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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d
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26 --species $species |
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27 --htmloutput $result_html |
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28 --htmloutputpath $result_html.extra_files_path |
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29 --htmltemplate ${__tool_directory__}/MetaMa_tpl.html |
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30 ]]> |
| 2 | 31 </command> |
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32 |
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33 <inputs> |
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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"/> |
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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d
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35 <param name="species" type="select" optionnal="false" label="species" help="species for annotation"> |
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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d
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36 <option value="org.Bt.eg.db">Bovine</option> |
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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d
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37 <option value="org.Cf.eg.db">Canine</option> |
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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d
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38 <option value="org.Gg.eg.db">Chicken</option> |
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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d
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39 <option value="org.Dm.eg.db">Fly</option> |
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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d
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40 <option value="org.Hs.eg.db">Human</option> |
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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d
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41 <option value="org.Mm.eg.db">Mouse</option> |
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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d
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42 <option value="org.Ss.eg.db">Pig</option> |
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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d
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43 <option value="org.Rn.eg.db">Rat</option> |
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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d
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44 <option value="org.Ce.eg.db">Worm</option> |
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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d
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45 <option value="org.Dr.eg.db">Zebrafish</option> |
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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d
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46 </param> |
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47 </inputs> |
| 2 | 48 |
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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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52 |
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53 <help> |
| 2 | 54 <![CDATA[ |
| 55 **What it does** | |
| 56 | |
| 57 Given several Rdata object this tool run a meta-analysis using the metaMA R package. | |
| 58 | |
| 59 **Results** | |
| 60 | |
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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 |
| 2 | 62 - A list of indicators to evaluate the quality of the performance of the meta-analysis |
| 63 | |
| 64 - DE : Number of differentially expressed genes | |
| 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 | |
| 66 - Loss : Number of genes that are identified differentially expressed in single studies but not in meta-analysis | |
| 67 - DR (Integration-driven Discovery Rate) : corresponding proportion of IDD | |
| 68 - IRR (Integration-driven Revision) : corresponding proportion of Loss | |
| 69 | |
| 70 - Fully sortable and requestable table, with gene annotations and hypertext links to NCBI gene database. | |
| 71 ]]> | |
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72 </help> |
| 2 | 73 |
| 74 </tool> |