view MetaRNAseq.xml @ 33:2d7595c8041d draft

planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71

<tool id="metarnaseq" name="RNA-seq data meta-analysis" version="1.1.0">

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

    <requirements>
        <requirement type="package">bioconductor-affy</requirement>
        <requirement type="package">bioconductor-annaffy</requirement>
        <requirement type="package">bioconductor-geoquery</requirement>
        <requirement type="package">r-venndiagram</requirement>
        <requirement type="package">r-jsonlite</requirement> 
        <requirement type="package">r-metarnaseq</requirement>
        <requirement type="package">r-optparse</requirement>
        <requirement type="package" version="1.3.3">r-upsetr</requirement>
    </requirements>	

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

    <command>

<![CDATA[   
        Rscript 
        ${__tool_directory__}/MetaRNASeq.R 
            --input "#for $s in $studies: 
                        ${s.input};${s.input.name};${s.nbreplicates}, 
                    #end for
"
            --fdr $fdr
            --result $top_table
            --htmloutput $result_html 
            --htmloutputpath $result_html.extra_files_path
            --htmltemplate ${__tool_directory__}/MetaRNASeq_tpl.html    
    ]]>

    </command>

    <inputs>
         <repeat name="studies" title="Study results" min="2" default="2" help="DESeq2 Result file and number of replicate of the study">
             <param format="tabular" name="input" multiple="false" type="data" optional="false" label="DESeq2 result file" help="Must have the same number of row in each study"/>
             <param name="nbreplicates" type="integer" value="10"  label="Number of replicates" help="Number of replicates of the study"/>
         </repeat>
         <param name="fdr" type="float" value="0.05" label="FDR" min="0" max="1" help="Adjusted p-value threshold to be declared differentially expressed"/>
    </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="result_html" label="Charts for ${tool.name} on ${on_string}"/>
    </outputs>
    
    <tests>
        
    </tests>

    <help>

    </help>

</tool>