view MetaRNAseq.xml @ 12:2da91c541ae4 draft

planemo upload commit ee50addaee7b7aa5c7b0305210875f489154791f-dirty

<tool id="metarnaseq" name="RNA-seq data meta-analysis">

    <description>perform meta-analysis thanks to metaRNAseq</description>

    <requirements>
        <requirement type="package" version="0.1.0">r-smagexp</requirement>
    </requirements>	

    <stdio>
        <exit_code range="1:" />
        <regex match="Warning" source="both" level="warning"/>
    </stdio>

	<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>