view ImportDataFromMatrix.xml @ 6:a2b8c2aabeb0 draft

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<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>