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<tool id="ReactomePA" name="ReactomePA" version="0.1.0">
    <description>Reactome Pathway Analysis</description>

    <requirements>
        <requirement type="package" version="1.20.3">r-getopt</requirement>
        <requirement type="package" version="1.34.0">bioconductor-ReactomePA</requirement>
        <requirement type="package" version="3.12.0">bioconductor-org.Hs.eg.db</requirement>
    </requirements>

    <command detect_errors="exit_code" interpreter="Rscript --vanilla"><![CDATA[
        $__tool_directory__/ReactomePA.R   
        -g '$gene_list_file' 
        -s '$Significant_Reactome_Pathway_result' 
        
        -o '$organism'
        
        -p '$adv.pvalueCutoff' 
        -w '$adv.pAdjustMethod' 
        #if $adv.convertId=="TRUE":
        -c
        #end if
        -i '$adv.minGSSize' 
        -a '$adv.maxGSSize'
    ]]></command>

    <inputs>
        <param type="data" name="gene_list_file" format="csv" label="Differentially expressed gene list" help="A csv file including a DEgenes column, that is, the Entrez ID of all differentially expressed genes." />
        <param type="select" name="organism" label="Organism" help="Choose organism. Only human, rat, mouse, celegans, yeast, zebrafish and fly are included.">
            <option value="human" selected="True">human (H sapiens)</option>
            <option value="rat">rat (R norvegicus)</option>
            <option value="mouse">house mouse (M musculus)</option>
            <option value="celegans">roundworm (C elegans)</option>
            <option value="yeast">yeast (S cerevisiae)</option>
            <option value="zebrafish">zebrafish (D rerio)</option>
            <option value="fly">fruit fly (D melanogaster)</option>
        </param>
        
        <section name="adv" title="Advanced Options" expanded="false">
            <param type="float" name="pvalueCutoff" value="0.05" min="0.00" max="1.00" label="P-value threshold" help="This is the cutoff p-value to determine significant enrichment of a pathway. Default is 0.05."/>
            <param type="select" name="pAdjustMethod" label="Method to adjust pathway p-values for multiple testing" help="Choose one method to adjust pathway p-values.">
                <option value="BH" selected="True">BH</option>
                <option value="holm">holm</option>
                <option value="hochberg">hochberg</option>
                <option value="hommel">hommel</option>
                <option value="bonferroni">bonferroni</option>
                <option value="BY">BY</option>
                <option value="fdr">fdr</option>
                <option value="none">none</option>
            </param>
            <param type="boolean" name="convertId" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Convert gene ID to SYMBOL" help="Select Yes if you want to convert entrez gene IDs to gene names (see the Help section below). Default: No." />
            <param type="integer" name="minGSSize" value="10" label="Minimum size of each geneSet" help="Gene sets with less genes than this value will be ignored."/>
            <param type="integer" name="maxGSSize" value="500" label="Maximum size of each geneSet" help="Gene sets with more genes than this value will be ignored." />
        </section>

    </inputs>
    
    <outputs>
        <data name="Significant_Reactome_Pathway_result" format="csv" label="Significant_Reactome_Pathway_result" />
    </outputs>

    <tests>
        <test>
            <param name="gene_list_file" value="Different_expression_gene.csv" ftype="csv" />
            <param name="organism" value="human"/>
            <param name="minGSSize" value="15"/>
            <param name="maxGSSize" value="200"/>
            <param name="pvalueCutoff" value="0.06"/>
            <param name="pAdjustMethod" value="holm"/>
            <param name="input7" value="true"/>
            <output name="Significant_Reactome_Pathway_result" file="t1.csv" ftype="csv" />
        </test>
    </tests>

    <help><![CDATA[

.. class:: infomark 

**What it does**

Reactome_ is a free, open-source, curated and peer-reviewed pathway database. 
Their goal is to provide intuitive bioinformatics tools for the visualization, 
interpretation and analysis of pathway knowledge. 

.. _Reactome: https://reactome.org

**ReactomePA** is a tool to enrich Significant Reactome Pathways with a list of differentially expressed genes.

This tool uses the function `enrichPathway` in the ReactomePA_ package.

.. _ReactomePA: http://www.bioconductor.org/packages/release/bioc/html/ReactomePA.html

---------

==========
**Inputs**
==========

Basic Options
--------------

**Differentially expressed gene list**

This tool requires a csv file which has a `DEgenes` column containing the entrez gene ID of all differentially expressed genes.

Example:

    ========== === 
    DEgenes     
    ========== === 
    4312
    8318
    10874
    55143
    55388
    991
    ========== === 

**Organism**

Choose the right organism for your data.  Only human, rat, mouse, celegans, yeast, zebrafish and fly are included.

Advanced Options
-----------------

**P-value threshold**

This is the cutoff p-value to determine significant enrichment of a pathway. Default is 0.05.

**Method to adjust pathway p-values for multiple testing**

Choose one method to adjust pathway p-values. Included methods are: `"BH"`, `"holm"`, `"hochberg"`, `"hommel"`, `"bonferroni"`, `"BY"`, `"fdr"` and `"none"`. Default is `"BH"`.

**Convert gene ID to SYMBOL**

If you want to convert entrez gene ID to gene SYMBOL name, choose Yes. Default: No.

**Minimum and maximum size of each geneSet**

Set minimum and maximum size of each gene set to be included in the analysis. Default are 10 and 500.

------

==========
**Output**
==========

A csv file including all enriched pathways.

Example - **Single Count Matrix**:

    =============== =============================================== =========== ===========
    ID               Description                                    GeneRatio   BgRatio
    =============== =============================================== =========== ===========
    R-HSA-69618     Mitotic Spindle Checkpoint                      22/326      113/10704
    R-HSA-2500257   Resolution of Sister Chromatid Cohesion         23/326      126/10704
    R-HSA-141424    Amplification of signal from the kinetochores	20/326      96/10704
    R-HSA-9648025   EML4 and NUDC in mitotic spindle formation		20/326      117/10704
    R-HSA-5663220   RHO GTPases Activate Formins                    21/326      140/10704
    =============== =============================================== =========== ===========
    

    ]]></help>
    
    <citations>
        <citation type="doi">10.1039/c5mb00663e</citation>
    </citations>
    
</tool>