view Analyse.xml @ 8:7f74250a083d draft

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<tool id="LimmaAnalyse" name="Limma analysis" version="0.3.0">
	<description>Perform gene expression analysis thanks to limma</description>
	<stdio>
        <exit_code range="1:" />
    </stdio>
	<requirements>
	  	<!--container type="docker">sblanck/smagexp</container-->
                <requirement type="package" version="0.1.0">r-smagexp</requirement>
	</requirements>
	<command>
		<![CDATA[ 
		Rscript
		${__tool_directory__}/Analyse.R
		   	--rdatainput ${rdataset}
			--conditions ${conditions}
		 	--selectcondition1 "${selectCondition1}"
		    --selectcondition2 "${selectCondition2}"
			--nbresult ${nbresult}
       		--rdataoutput ${result_export_eset}
       		--htmloutput $result_html 
			--htmloutputpath $result_html.files_path
			--tabularoutput $result_tabular
			--htmltemplate ${__tool_directory__}/Analyse_tpl.html
		]]>
	</command>
	
	<inputs>
		<param name="rdataset" type="data" format="rdata" label="RData" help="RData to be used"/>
		<param name="conditions" type="data" format="cond" label="Conditions" help="conditions associated with the rData file"/>
		<param name="selectCondition1" type="select" label="condition 1">
			<options from_dataset="conditions">
    		<column name="name" index="1"/>
    		<column name="value" index="1"/>
    		<filter type="unique_value" column="1"/>
		</options>
		</param>
		<!--param name="condition1" type="select" display="checkboxes" label="Condition 1" multiple="true">
			<options from_dataset="conditions">
    		<column name="name" index="2"/>
    		<column name="value" index="0"/>
			<filter  type="param_value" ref="selectCondition1" column="1"/>
		</options>
		</param-->	
		<param name="selectCondition2" type="select" label="condition 2">
			<options from_dataset="conditions">
    		<column name="name" index="1"/>
    		<column name="value" index="1"/>
			<filter type="unique_value" column="1"/>    		
		</options>
		</param>	
		<!--param name="condition2" type="select" display="checkboxes" label="Condition 2" multiple="true">
			<options from_dataset="conditions">
    		<column name="name" index="2"/>
    		<column name="value" index="0"/>
			<filter  type="param_value" ref="selectCondition2" column="1"/>
		</options>
		</param-->	
		<param name="nbresult" type="integer" value="1000" min="1" label="number of top genes" help="Number of genes to be displayed in result datatable"/>
	</inputs>
	<outputs>
		<data format="html" name="result_html" label="Results of analysis of ${rdataset.name}"/>
		<data format="rdata" name="result_export_eset" label="Export of expression set of ${rdataset.name}"/>
		<data format="tabular" name="result_tabular" label="Text Results of analysis of ${rdataset.name}"/>
		
	</outputs>
	<help>
<![CDATA[ 
**What it does**
		
The Limma analysis tool performs single analysis either of data previously retrieved from GEO database or normalized affymetrix .CEL files data. 
Given a .cond file, it runs a standard limma differential expression analysis. 

**Example** of .cond file      	

The .cond file should look like this 
::


 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**
		
- Boxplots, p-value histograms and a volcano plot 
- Table summarizing the differentially expressed genes and their annotations. This table is sortable and requestable.
- Rdata object to perform further meta-analysis. 
]]>
	</help>

</tool>