diff ImportDataFromMatrix.xml @ 2:93451f832736 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ImportDataFromMatrix.xml	Tue Mar 21 10:28:47 2017 -0400
@@ -0,0 +1,79 @@
+<tool id="importMatrixData" name="Import custom data">
+	<description>Quality control and normalization of a custom matrix expression data</description>
+	<requirements>
+	  	<!--container type="docker">sblanck/smagexp</container-->
+		<requirement type="package" version="0.1.0">r-smagexp</requirement>		
+	</requirements>
+	<command interpreter="python">
+		<![CDATA[ 
+		stderr_wrapper.py Rscript 
+		${__tool_directory__}/ImportDataFromMatrix.R
+		    $input
+			$normalization
+			$conditions
+			$annotations
+			$result_export_eset
+       		$result_html
+			$result_html.files_path
+		${__tool_directory__}/ImportDataFromMatrix_tpl.html
+		]]>		
+		</command>
+		
+	
+	<inputs>
+		<param name="input" type="data" format="tabular" label="Input data" help="Input data"/>
+		<param name="normalization" type="select" label="Preprocessing/normalization">
+    		<option value="quantile">quantile normalization + log2</option>
+            <option value="log2">log2 only</option>
+            <option value="none">none</option>
+		</param>
+		<param name="conditions" type="data" format="cond" label="Conditions" help="conditions associated with the input file"/>
+		<param name="annotations" type="text" label="Annotation GPL code" help="GPL code for annotations"/>		
+	</inputs>
+
+	<outputs>
+		<data format="rdata" name="result_export_eset" label="export normalized expressionSet"/>		
+		<data format="html" name="result_html" label="QC result"/>
+	</outputs>
+
+	<help>
+<![CDATA[ 
+**What it does**
+		     	
+This tool imports data stored in a tabular text file. 
+Column titles (chip IDs) must match the IDs of the .cond file.
+GPL annotation code is also required to fetch annotations from GEO.
+
+**Exemple**
+
+Header of input tabular text file
+::
+
+""	"GSM80460"	"GSM80461"	"GSM80462"	"GSM80463"	"GSM80464"
+"1007_s_at"	-0.0513991525066443	0.306845500314283	0.0854246562526777	-0.142417044615852	0.0854246562526777
+"1053_at"	-0.187707155126729	-0.488026018218199	-0.282789700980404	0.160920188181103	0.989865622866287
+"117_at"	0.814755482809874	-2.15842936260448	-0.125006361067033	-0.256700472111743	0.0114956388378294
+"121_at"	-0.0558912008920451	-0.0649174766813385	0.49467161164755	-0.0892673380970874	0.113700499164728
+"1294_at"	0.961993677420255	-0.0320936297098533	-0.169744675832317	-0.0969617298870879	-0.181149439104566
+"1316_at"	0.0454429707611671	0.43616183931445	-0.766111939825723	-0.182786075741673	0.599317793698226
+"1405_i_at"	2.23450132056221	0.369606070031838	-1.06190243892591	-0.190997225060914	0.595503660502742
+
+
+The .cond file should look like this 
+::
+
+ Sample ID 	Condition			Description
+ GSM80460	series of 16 tumors	GSM80460 OSCE-2T SERIES OF 16 TUMORS
+ GSM80461	series of 16 tumors	GSM80461 OSCE-4T Series of 16 Tumors
+ GSM80462	series of 16 tumors	GSM80462 OSCE-6T Series of 16 Tumors
+ GSM80476	series of 4 normals	GSM80476 OSCE-2N Series of 4 Normals
+ GSM80477	series of 4 normals	GSM80477 OSCE-9N Series of 4 Normals
+
+				
+**Results**
+	- Bboxplots and MA plots 
+	- Rdata object containing the data for further analysis.
+]]>
+	</help>
+
+</tool>