diff MetaRNAseq.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/MetaRNAseq.xml	Thu Feb 22 08:38:22 2018 -0500
@@ -0,0 +1,50 @@
+<tool id="metarnaseq" name="RNA-seq data meta-analysis" version="1.0.0">
+
+    <description>Performs meta-analysis thanks to metaRNAseq</description>
+
+    <requirements>
+        <requirement type="package">bioconductor-affy</requirement>
+        <requirement type="package">bioconductor-annaffy</requirement>
+        <requirement type="package">bioconductor-geoquery</requirement>
+        <requirement type="package">r-venndiagram</requirement>
+        <requirement type="package">r-jsonlite</requirement> 
+        <requirement type="package">r-metarnaseq</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__}/MetaRNASeq.R 
+            --input "#for $input in $inputs# $input;$input.name, #end for#"
+            --result $top_table
+            --htmloutput $result_html 
+            --htmloutputpath $result_html.extra_files_path
+            --htmltemplate ${__tool_directory__}/MetaRNASeq_tpl.html	
+    ]]>	
+    </command>
+
+    <inputs>
+        <param format="tabular" name="inputList" multiple="true" type="data" optional="false" label="Counts file" help="Must have the same number of row in each study. The experimental conditions must be specified in the header of each file"/>
+    </inputs>
+
+    <outputs>
+        <data format="tabular" name="top_table" label="Summary of meta-analysis and single studie analysis from ${tool.name} on ${on_string}"/>
+        <data format="html" name="diagnostic_html" label="Charts for ${tool.name} on ${on_string}"/>
+    </outputs>
+    
+    <tests>
+        
+    </tests>
+
+    <help>
+
+    </help>
+
+</tool>