view MetaRNAseq.xml @ 14:e5a94bc69bd6 draft

planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160

<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>

    <![CDATA[ 	
        Rscript 
        ${__tool_directory__}/MetaRNASeq.R 
            --input "#for $input in $inputs# $input;$input.name, #end for#"
            --result $top_table
            --htmloutput $result_html 
            --htmloutputpath $result_html.extra_files_path
            --htmltemplate ${__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>
    
    <tests>
        
    </tests>

    <help>

    </help>

</tool>