<tool id="edu.tamu.cpt2.helicalWheel.generateHelicalWheel" name="Helical Wheel" version="1.0">
    <description>Generate and Plot a Protein Helical Wheel</description>
    <macros>
    
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package">numpy</requirement>
        <requirement type="package">pandas</requirement>
        <requirement type="package" version="0.18.1">scikit-learn</requirement>
        <requirement type="package">scipy</requirement>
        <requirement type="package">matplotlib</requirement>
    </expand>
    <command detect_errors="aggressive"><![CDATA[
python '$__tool_directory__/generateHelicalWheel.py'
--sequence '$sequence'
--seqRange '$seqRange'
--t_size '$t_size'
--rotation '$rotation'
'$numbering'
--f_A "$sec_B.f_A"
--f_C "$sec_C.f_C"
--f_D "$sec_D.f_D"
--f_E "$sec_D.f_E"
--f_F "$sec_B.f_F"
--f_G "$sec_C.f_G"
--f_H "$sec_E.f_H"
--f_I "$sec_B.f_I"
--f_K "$sec_E.f_K"
--f_L "$sec_B.f_L"
--f_M "$sec_B.f_M"
--f_N "$sec_C.f_N"
--f_P "$sec_B.f_P"
--f_Q "$sec_C.f_Q"
--f_R "$sec_E.f_R"
--f_S "$sec_C.f_S"
--f_T "$sec_C.f_T"
--f_V "$sec_B.f_V"
--f_W "$sec_B.f_W"
--f_Y "$sec_C.f_Y"
--t_A "$sec_B.t_A"
--t_C "$sec_C.t_C"
--t_D "$sec_D.t_D"
--t_E "$sec_D.t_E"
--t_F "$sec_B.t_F"
--t_G "$sec_C.t_G"
--t_H "$sec_E.t_H"
--t_I "$sec_B.t_I"
--t_K "$sec_E.t_K"
--t_L "$sec_B.t_L"
--t_M "$sec_B.t_M"
--t_N "$sec_C.t_N"
--t_P "$sec_B.t_P"
--t_Q "$sec_C.t_Q"
--t_R "$sec_E.t_R"
--t_S "$sec_C.t_S"
--t_T "$sec_C.t_T"
--t_V "$sec_B.t_V"
--t_W "$sec_B.t_W"
--t_Y "$sec_C.t_Y"
--output '$output'
]]></command>
    <inputs>
        <param label="Paste in exact sequence to be plotted" name="sequence" type="text"/>
        <param label="Label Start Number" name="seqRange" type="integer" value="1" help="starting residue number to use for labels"/>
        <param label="Amino Acid Text Size" name="t_size" type="integer" value="32" help="Alters the Text Size. Default is 32"/>
        <param label="Rotation" name="rotation" type="integer" value="90" help="Rotates the helical wheel. Default is 90"/>
        <param label="Label Numbering Text" name="numbering" type="boolean" help="number schema subscripts" truevalue="--numbering" falsevalue=""/>
        <section name="sec_B" title="nonpolar ; hydrophobic">
            <param name="f_A" type="color" label="Color for A" value="#ffcc33">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="t_A" type="color" label="Text color for A" value="#000000">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="f_F" type="color" label="Color for F" value="#ffcc33">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="t_F" type="color" label="Text color for F" value="#000000">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="f_I" type="color" label="Color for I" value="#ffcc33">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="t_I" type="color" label="Text color for I" value="#000000">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="f_L" type="color" label="Color for L" value="#ffcc33">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="t_L" type="color" label="Text color for L" value="#000000">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="f_M" type="color" label="Color for M" value="#ffcc33">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="t_M" type="color" label="Text color for M" value="#000000">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="f_P" type="color" label="Color for P" value="#ffcc33">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="t_P" type="color" label="Text color for P" value="#000000">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="f_V" type="color" label="Color for V" value="#ffcc33">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="t_V" type="color" label="Text color for V" value="#000000">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="f_W" type="color" label="Color for W" value="#ffcc33">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="t_W" type="color" label="Text color for W" value="#000000">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
        </section>
        <section name="sec_C" title="polar ; uncharged">
            <param name="f_C" type="color" label="Color for C" value="#b5b5b5">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="t_C" type="color" label="Text color for C" value="#000000">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="f_G" type="color" label="Color for G" value="#b5b5b5">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="t_G" type="color" label="Text color for G" value="#000000">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="f_N" type="color" label="Color for N" value="#b5b5b5">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="t_N" type="color" label="Text color for N" value="#000000">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="f_Q" type="color" label="Color for Q" value="#b5b5b5">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="t_Q" type="color" label="Text color for Q" value="#000000">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="f_S" type="color" label="Color for S" value="#b5b5b5">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="t_S" type="color" label="Text color for S" value="#000000">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="f_T" type="color" label="Color for T" value="#b5b5b5">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="t_T" type="color" label="Text color for T" value="#000000">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="f_Y" type="color" label="Color for Y" value="#b5b5b5">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="t_Y" type="color" label="Text color for Y" value="#000000">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
        </section>
        <section name="sec_D" title="polar ; acidic (negatively charged)">
            <param name="f_D" type="color" label="Color for D" value="#db270f">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="t_D" type="color" label="Text color for D" value="#FFFFFF">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="f_E" type="color" label="Color for E" value="#db270f">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="t_E" type="color" label="Text color for E" value="#FFFFFF">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
        </section>
        <section name="sec_E" title="polar ; basic (positive charge)">
            <param name="f_H" type="color" label="Color for H" value="#12d5fc">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="t_H" type="color" label="Text color for H" value="#000000">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="f_K" type="color" label="Color for K" value="#12d5fc">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="t_K" type="color" label="Text color for K" value="#000000">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="f_R" type="color" label="Color for R" value="#12d5fc">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
            <param name="t_R" type="color" label="Text color for R" value="#000000">
                <sanitizer>
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="#"/>
                    </valid>
                </sanitizer>
            </param>
        </section>
    </inputs>
    <outputs>
        <data format="png" name="output" label="_helicalWheel.png"/>
    </outputs>
    <help><![CDATA[
**What it does**
INPUT : Peptide Sequence
PARAMETERS : 
primary parameters : 
> Paste in exact sequence to be plotted - Input Sequence of desired helical wheel plot
> Label Start Number - Numerical value that represents the beginning of the sequence (default 1)
> Amino Acid Text Size - Size of text for helical wheel (default 32)
> Rotation - Degrees to rotate helical wheel (defaul 90)
color parameters : 
> Background Color and Text Color Selections
METHOD : Using the core features from the modlAMP python module, a helical wheel projection is constructed.
OUTPUT : _helicalWheel.png
NOTES : Peptide lengths longer than 36 residues will not properly graph.
]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btx285</citation>
        <citation type="bibtex">
        @unpublished{galaxyTools,
            author = {C. Ross},
            title = {CPT Galaxy Tools},
            year = {2020-},
            note = {https://github.com/tamu-cpt/galaxy-tools/}
        }
        </citation>
    </citations>
</tool>