Mercurial > repos > sblanck > smagexp
comparison MetaMA.xml @ 0:1024245abc70 draft
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
| author | sblanck |
|---|---|
| date | Thu, 22 Feb 2018 08:38:22 -0500 |
| parents | |
| children | 3ce32282f6a4 |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:1024245abc70 |
|---|---|
| 1 <tool id="metaMA" name="Microarray data meta-analysis" version="1.0.0"> | |
| 2 | |
| 3 <description>Performs meta-analysis thanks to metaMA.</description> | |
| 4 | |
| 5 <requirements> | |
| 6 <requirement type="package">bioconductor-affy</requirement> | |
| 7 <requirement type="package">bioconductor-annaffy</requirement> | |
| 8 <requirement type="package">bioconductor-geoquery</requirement> | |
| 9 <requirement type="package">bioconductor-org.hs.eg.db</requirement> | |
| 10 <requirement type="package">r-venndiagram</requirement> | |
| 11 <requirement type="package">r-metama</requirement> | |
| 12 <requirement type="package">r-optparse</requirement> | |
| 13 </requirements> | |
| 14 | |
| 15 <stdio> | |
| 16 <exit_code range="1:" /> | |
| 17 <regex match="Warning" source="both" level="warning"/> | |
| 18 </stdio> | |
| 19 | |
| 20 <command> | |
| 21 <![CDATA[ | |
| 22 Rscript | |
| 23 ${__tool_directory__}/MetaMA.R | |
| 24 --input $input | |
| 25 --species $species | |
| 26 --htmloutput $result_html | |
| 27 --htmloutputpath $result_html.extra_files_path | |
| 28 --htmltemplate ${__tool_directory__}/MetaMa_tpl.html | |
| 29 ]]> | |
| 30 </command> | |
| 31 | |
| 32 <inputs> | |
| 33 <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"/> | |
| 34 <param name="species" type="select" optionnal="false" label="species" help="species for annotation"> | |
| 35 <option value="org.Bt.eg.db">Bovine</option> | |
| 36 <option value="org.Cf.eg.db">Canine</option> | |
| 37 <option value="org.Gg.eg.db">Chicken</option> | |
| 38 <option value="org.Dm.eg.db">Fly</option> | |
| 39 <option value="org.Hs.eg.db">Human</option> | |
| 40 <option value="org.Mm.eg.db">Mouse</option> | |
| 41 <option value="org.Ss.eg.db">Pig</option> | |
| 42 <option value="org.Rn.eg.db">Rat</option> | |
| 43 <option value="org.Ce.eg.db">Worm</option> | |
| 44 <option value="org.Dr.eg.db">Zebrafish</option> | |
| 45 </param> | |
| 46 </inputs> | |
| 47 | |
| 48 <outputs> | |
| 49 <data format="html" name="result_html" label="Meta-analysis results"/> | |
| 50 </outputs> | |
| 51 | |
| 52 <help> | |
| 53 <![CDATA[ | |
| 54 **What it does** | |
| 55 | |
| 56 Given several Rdata object this tool run a meta-analysis using the metaMA R package. | |
| 57 | |
| 58 **Results** | |
| 59 | |
| 60 - Venn Diagram summarizing the results of the meta-analysis | |
| 61 - A list of indicators to evaluate the quality of the performance of the meta-analysis | |
| 62 | |
| 63 - DE : Number of differentially expressed genes | |
| 64 - 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 | |
| 65 - Loss : Number of genes that are identified differentially expressed in single studies but not in meta-analysis | |
| 66 - DR (Integration-driven Discovery Rate) : corresponding proportion of IDD | |
| 67 - IRR (Integration-driven Revision) : corresponding proportion of Loss | |
| 68 | |
| 69 - Fully sortable and requestable table, with gene annotations and hypertext links to NCBI gene database. | |
| 70 ]]> | |
| 71 </help> | |
| 72 | |
| 73 </tool> |