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

> $html ]]>
</command>
    <inputs>
        <expand macro="input/fasta/protein"/>
        <param label="Output format" name="svg" type="select">
            <option value="">HTML</option>
            <option value="--svg">SVG</option>
        </param>
        <conditional name="scheme">
            <param label="Colour scheme" name="cs" type="select">
                <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>
            </param>
            <when value="default"/>
            <when value="rb"/>
            <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"/>
            </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"/>
        </test>
    </tests>
    <help>
**What it does**

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