<tool id="ks_distribution" name="KsDistribution" version="1.0.1">
    <description>plots the distribution of synonymous substitution (Ks) rates and fits significant component(s)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements_ks_distribution" />
    <command detect_errors="exit_code"><![CDATA[
Rscript $__tool_directory__/ks_distribution.R
-k '$input'
-c '$components'
-n $components.metadata.number_comp
-o '$output'
#if str($choose_colors_cond.choose_colors) == 'yes':
    #set specified_colors = list()
    #for $selection in $choose_colors_cond.colors:
        $specified_colors.append(str($selection.color))
    #end for
    #set specified_colors = ",".join($specified_colors)
    -s '$specified_colors'
#end if
    ]]></command>
    <inputs>
        <param name="input" format="tabular" type="data" label="KaKsAnalysis tabular file" />
        <param name="components" format="ptkscmp" type="data" label="Significant components" />
        <conditional name="choose_colors_cond">
            <param name="choose_colors" type="select" label="Choose colors for significant components">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <repeat name="colors" title="Component colors" min="1">
                    <param name="color" type="select" label="Color">
                        <option value="red" selected="True">red</option>
                        <option value="green">green</option>
                        <option value="blue">blue</option>
                        <option value="yellow">yellow</option>
                        <option value="darkorange">dark orange</option>
                        <option value="black">black</option>
                    </param>
                </repeat>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format="pdf"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="kaks_input1.tabular" ftype="tabular" />
            <param name="components" value="components.ptkscmp" ftype="ptkscmp" />
            <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
        </test>
    </tests>
    <help>
**What it does**
 
This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary analyses of
genome-scale gene families and transcriptomes.  This tool uses the analysis results produced by the KaKsAnalysis tool to plot the
distribution of synonymous substitution (Ks) rates and fit the estimated significant normal mixtures component(s) onto the distribution.

-----

**Options**

 * **Synonymous substitution rates** - estimated synonymous substitution (Ks) rates output file produced by the KaKsAnalysis tool selected from your history.
 * **Synonymous components** - estimated significant component(s) output file produced by the KaKsAnalysis tool selected from your history.
 * **Choose colors for significant components** - select 'Yes' to specify component colors or 'No' for colors chosen randlomly.

   * **Component colors** - select a color from the palette for each component (colors will be chosen randomly for unspecified components).
    </help>
    <citations>
        <expand macro="citation1" />
        <citation type="bibtex">
            @article{Wall2008,
            journal = {Nucleic Acids Research},
            author = {2. Wall PK, Leebens-Mack J, Muller KF, Field D, Altman NS},
            title = {PlantTribes: a gene and gene family resource for comparative genomics in plants},
            year = {2008},
            volume = {36},
            number = {suppl 1},
            pages = {D970-D976},}
        </citation>
        <citation type="bibtex">
            @article{Altschul1990,
            journal = {Journal of molecular biology}
            author = {3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ},
            title = {Basic local alignment search tool},
            year = {1990},
            volume = {215},
            number = {3},
            pages = {403-410},}
        </citation>
        <citation type="bibtex">
            @article{Katoh2013,
            journal = {Molecular biology and evolution},
            author = {4. Katoh K, Standley DM},
            title = {MAFFT multiple sequence alignment software version 7: improvements in performance and usability},
            year = {2013},
            volume = {30},
            number = {4},
            pages = {772-780},}
        </citation>
        <citation type="bibtex">
            @article{Yang2007,
            journal = {Molecular biology and evolution},
            author = {5. Yang Z},
            title = {PAML 4: phylogenetic analysis by maximum likelihood},
            year = {2007},
            volume = {24},
            number = {8},
            pages = {1586-1591},}
        </citation>
        <citation type="bibtex">
            @article{Cui2006,
            journal = {Genome Research},
            author = {6. Cui L, Wall PK, Leebens-Mack JH, Lindsay BG, Soltis DE, Doyle JJ, Soltis PS, Carlson JE, Arumuganathan K, Barakat A, Albert VA},
            title = {Widespread genome duplications throughout the history of flowering plants},
            year = {2006},
            volume = {16},
            number = {6},
            pages = {738-749},}
        </citation>
        <citation type="bibtex">
            @article{McLachlan1999,
            journal = {Journal of Statistical Software},
            author = {7. McLachlan GJ, Peel D, Basford KE, Adams P},
            title = {The EMMIX software for the fitting of mixtures of normal and t-components},
            year = {1999},
            volume = {4},
            number = {2},
            pages = {1-14},}
        </citation>
    </citations>
</tool>