<tool id="plot_comparative" name="Visualization of comparative clustering"
      version="1.0.0.3">
    <description>Simple utility to create visualization of RepeatExplorer conmparative
        analysis
    </description>
    <requirements>
        <requirement type="package">r-optparse</requirement>
    </requirements>
    <required_files>
        <include type="literal" path="plot_comparative_clustering_summary.R"/>
    </required_files>
    <command detect_errors="exit_code">
        Rscript '$__tool_directory__'/plot_comparative_clustering_summary.R
        --cluster_table=$cluster_table
        --comparative_counts=$counts
        --number_of_colors=$number_of_colors
        --output=$outpdf
        $nuclear_only
        #if $normalization.use_genome_size:
        --genome_size $normalization.genome_size_table
        #end if
    </command>

    <inputs>
        <param format="txt" type="data" name="cluster_table"
               label="file from RepeatExplorer2 clustering - CLUSTER_TABLE.csv"/>
        <param format="txt" type="data" name="counts"
               label="file from RepeatExplorer2 output - COMPARATIVE_ANALYSIS_COUNTS.csv"/>
        <param value="10" min="2" max="20" type="integer" name="number_of_colors"
               label="Maximum number of color used for plottting"/>
        <param value="false" type="boolean" truevalue="--nuclear_only" falsevalue=""
               name="nuclear_only"
               label="Remove all non-nuclear sequences (organel and contamination)"/>
        <conditional name="normalization">
            <param name="use_genome_size" type="boolean" checked="False"
                   label="Normalize to genome size"
                   help="Note that if this option is used, non-nuclear sequences are always removed."/>
            <when value="false">
                <!-- pass -->
            </when>
            <when value="true">
                <param name="genome_size_table" type="data" format="txt"
                       label="table with genome sizes"/>

            </when>

        </conditional>
    </inputs>

    <outputs>
        <data format="pdf" name="outpdf" label="Comparative analysis summary"/>
    </outputs>
    <help>
        **Visualization of comparative clustering**
        Visualization can be created two output files from RepeatExplorer pipeline.

        Input file CLUSTER_TABLE.csv contains automatic annotation, information about
        cluster sizes and the total number of reads used for analysis
        Example of CLUSTER_TABLE.csv: ::

        "Number_of_reads_in_clusters" 3002
        "Number_of_clusters" 895
        "Number_of_superclusters" 895
        "Number_of_singlets" 6998

        "Number_of_analyzed_reads" 10000

        "Cluster" "Supercluster" "Size" "Size_adjusted" "Automatic_annotation"
        "TAREAN_classification" "Final_annotation"
        1 1 61 61 "All" "Other"
        2 2 59 59 "All/repeat/satellite" "Putative satellites (high confidence)"
        3 3 45 45 "All/repeat/satellite" "Putative satellites (low confidence)"
        4 4 38 38 "All" "Other"
        5 5 32 32 "All" "Other"
        6 6 28 28 "All" "Other"
        7 7 25 25 "All" "Other"
        8 8 24 24 "All" "Other"
        9 9 23 23 "All" "Other"
        10 10 22 22
        "All/repeat/mobile_element/Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre"
        "Other"
        11 11 20 20 "All" "Other"
        12 12 20 20 "All" "Other"


    </help>
</tool>