diff Recount.xml @ 6:3ce32282f6a4 draft

planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 228bd64b01f184d5d8ebc9f65fe0add2d45ed4fe

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Recount.xml	Tue Jun 26 08:54:45 2018 -0400
@@ -0,0 +1,52 @@
+<tool id="Recount" name="Recount" version="1.0.0">
+
+    <description>Get rna-seq count data with R recount Package</description>
+
+    <requirements>
+        <requirement type="package">bioconductor-recount</requirement>
+        <requirement type="package">r-optparse</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+        <regex match="Warning" source="both" level="warning"/>
+    </stdio>
+
+    <command>
+        <![CDATA[ 
+        Rscript --vanilla
+        ${__tool_directory__}/Recount.R 
+            --id ${recountID}
+            --report ${report}
+        ]]>
+    </command>
+
+    <inputs>
+        <param name="recountID" type="text" size="12" optional="false" label="Recount ID" help="">
+            <validator type="empty_field"/>
+        </param>
+     </inputs>
+
+    <outputs>
+    <data format="txt" name="report">
+        <discover_datasets pattern="__designation_and_ext__" format="tabular" directory="split" visible="true" />
+    </data>
+</outputs>
+
+    <tests>
+    </tests>
+
+    <help>
+<![CDATA[ 
+**What it does**     	
+
+This tool fetches RNA-seq count data directly from Recount project based on the recount bioconductor R package. Given an ID, it returns a small report 
+containing the metadata of the experiment. Il also generates one count file per sample.
+
+**Results**
+	
+- Tabular file containing samples ID and samples conditions
+- One count file per sample
+]]> 		
+    </help>
+
+</tool>