diff MetaMA.xml @ 0:1024245abc70 draft

planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MetaMA.xml	Thu Feb 22 08:38:22 2018 -0500
@@ -0,0 +1,73 @@
+<tool id="metaMA" name="Microarray data meta-analysis" version="1.0.0">
+
+    <description>Performs meta-analysis thanks to metaMA.</description>
+
+    <requirements>
+        <requirement type="package">bioconductor-affy</requirement>
+        <requirement type="package">bioconductor-annaffy</requirement>
+        <requirement type="package">bioconductor-geoquery</requirement>
+        <requirement type="package">bioconductor-org.hs.eg.db</requirement>
+        <requirement type="package">r-venndiagram</requirement>
+        <requirement type="package">r-metama</requirement>
+        <requirement type="package">r-optparse</requirement>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" />
+        <regex match="Warning" source="both" level="warning"/>
+    </stdio>
+
+    <command>
+        <![CDATA[ 
+        Rscript 
+        ${__tool_directory__}/MetaMA.R
+            --input $input
+            --species $species
+            --htmloutput $result_html 
+            --htmloutputpath $result_html.extra_files_path
+            --htmltemplate ${__tool_directory__}/MetaMa_tpl.html
+        ]]>
+	</command>
+
+    <inputs>
+        <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"/>
+        <param name="species" type="select" optionnal="false" label="species" help="species for annotation">
+            <option value="org.Bt.eg.db">Bovine</option>
+            <option value="org.Cf.eg.db">Canine</option>
+            <option value="org.Gg.eg.db">Chicken</option>
+            <option value="org.Dm.eg.db">Fly</option>
+            <option value="org.Hs.eg.db">Human</option>
+            <option value="org.Mm.eg.db">Mouse</option>
+            <option value="org.Ss.eg.db">Pig</option>
+            <option value="org.Rn.eg.db">Rat</option>
+            <option value="org.Ce.eg.db">Worm</option>
+            <option value="org.Dr.eg.db">Zebrafish</option>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data format="html" name="result_html" label="Meta-analysis results"/>
+    </outputs>
+
+    <help>
+<![CDATA[ 
+**What it does**
+		
+Given several Rdata object this tool run a meta-analysis using the metaMA R package.
+		
+**Results**
+		
+- Venn Diagram summarizing the results of the meta-analysis
+- A list of indicators to evaluate the quality of the performance of the meta-analysis
+		
+	- DE : Number of differentially expressed genes 
+	- 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
+	- Loss : Number of genes that are identified differentially expressed in single studies but not in meta-analysis 
+	- DR (Integration-driven Discovery Rate) : corresponding proportion of IDD
+	- IRR (Integration-driven Revision) : corresponding proportion of Loss
+		
+- Fully sortable and requestable table, with gene annotations and hypertext links to NCBI gene database.
+]]>
+    </help>
+
+</tool>