view MetaRNAseq.xml @ 4:2c9e44ff68dc draft

use optparse

<tool id="metarnaseq" name="RNA-seq data meta-analysis">
	<description>perform meta-analysis thanks to metaRNAseq</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__}/MetaRNASeq.R 
		#for $currentInput in $inputList
        	"${currentInput}"
			"${currentInput.name}"	
		 #end for	
			$top_table 
			$diagnostic_html 
			"$diagnostic_html.files_path"
		${__tool_directory__}/MetaRNASeq_tpl.html
	]]>	
	</command>

	<inputs>
		<param format="tabular" name="inputList" multiple="true" type="data" optional="false" label="Counts file" help="Must have the same number of row in each study. The experimental conditions must be specified in the header of each file"/>
	</inputs>

	<outputs>
		<data format="tabular" name="top_table" label="Summary of meta-analysis and single studie analysis from ${tool.name} on ${on_string}"/>
		<data format="html" name="diagnostic_html" label="Charts for ${tool.name} on ${on_string}"/>
	</outputs>

	<help>
		
	</help>

</tool>