<tool id="edu.tamu.cpt.tools.charges" name="Charges" version="2.0">
    <description>colour sequences based on rules</description>
    <macros>
        <import>macros.xml</import>
    
    </macros>
    <expand macro="requirements"> </expand>
    <command detect_errors="aggressive"><![CDATA[
python '$__tool_directory__/fasta_charges.py'
'$svg'
@SEQUENCE@ 

--width '$width'

#if $scheme.cs == "default":
    --aa HSQTNCY AVILMPFWG ERDK
    --fgColor "#000000" "#000000" "#ffffff"
    --bgColor "#ffffff" "#999999" "#000000"
#elif $scheme.cs == "rb":
    --aa KR ED HSQTNCYAVILMPFWG
    --fgColor "#ffffff" "#ffffff" "#000000"
    --bgColor "#00b0f0" "#fc0000" "#ffffff"
#elif $scheme.cs == "rbgb":
    --aa KR ED P C HSQTNYAVILMFWG
    --fgColor "#ffffff" "#ffffff" "#ffffff" "#ffffff" "#000000"
    --bgColor "#00b0f0" "#fc0000" "#1cb026" "#805839" "#ffffff"
#else:
    --aa
    #for group in $scheme.groups:
        "$group.aminoAcids"
    #end for
    --fgColor
    #for group in $scheme.groups:
        "$group.fgColour"
    #end for
    --bgColor
    #for group in $scheme.groups:
        "$group.bgColour"
    #end for
#end if
]]></command>
    <inputs>
        <expand macro="input/fasta/protein"></expand>
        <label for="output-format">Output format</label>
        <select id="output-format" name="svg">
            <option value="">HTML</option>
            <option value="--svg">SVG</option>
        </select>
        <conditional name="scheme">
            <label for="Colour scheme">Colour scheme</label>
            <select id="Colour scheme" name="cs">
                <option value="default">Default hyrophobic/polar/charged</option>
                <option value="rb">Positives Blue, Negatives Red</option>
                <option value="rbgb">Positives Blue, Negatives Red, Prolines Green, Cysteines Brown</option>
                <option value="custom">Custom Colour Scheme</option>
            </select>
            <when value="default"></when>
            <when value="rb"></when>
            <when value="custom">
                <repeat name="groups" title="Colour Group">
                    <param name="aminoAcids" type="text" label="Amino Acids" help="Amino acids to colour a specific colour"/>
                    <param name="fgColour" type="color" label="Foreground Color"/>
                    <param name="bgColour" type="color" label="Background Color"/>
                </repeat>
            </when>
        </conditional>
        <param label="Plot width" name="width" type="integer" value="120"/>
    </inputs>
    <outputs>
        <data format="html" name="html">
            <change_format>
                <when input="svg" value="--svg" format="svg"></when>
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="sequences" value="prot.fa"/>
            <param name="cs" value="default"/>
            <param name="width" value="120"/>
            <output name="html" file="charges.html"></output>
        </test>
    </tests>
    <help>
**What it does**

Colors fasta (protein) sequences based on rules, and displays outputs as HTML.
</help>
    <expand macro="citations"></expand>
</tool>