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Imported from capsule None
author sblanck
date Wed, 13 Apr 2016 07:40:02 -0400
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<tool id="metaMAGEOQuery" name="GEOanalyse" version="0.1.0">
	<description>GEOAnalyse wrapper</description>
	<requirements>
	  <container type="docker">sblanck/testtool:latest</container>
	</requirements>
	<command>

		/galaxy-tools/stderr_wrapper.py Rscript 
		/galaxy-tools/transcriptomics/GEOanalyse/GEOAnalyse.R
		   	"${rdataset}"
		 	"${selectCondition}"
       		$result_html 
			$result_html.files_path
		/galaxy-tools/transcriptomics/GEOanalyse/GEOAnalyse_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="selectCondition" type="select" label="case condition">
			<options from_dataset="conditions">
    		<column name="name" index="0"/>
    		<column name="value" index="0"/>
		</options>
		</param>	
	
	</inputs>
	<outputs>
		<data format="html" name="result_html" label="Annotations"/>
		
	</outputs>

	<help>
		NOTE: This metaMA wrapper performs p-value combination from multiples studies with the same probes. If you need to normalize your data, use "matrix_normalisation" tool on each file. Then, use "Merge Standard datasets(copied)" tool to make a multiple file dataset.
	</help>

</tool>