Mercurial > repos > cpt > cpt_helical_wheel
diff generateHelicalWheel.xml @ 1:9b276485c94a draft
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
| author | cpt |
|---|---|
| date | Mon, 05 Jun 2023 02:44:43 +0000 |
| parents | |
| children | e9fb56f44c35 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generateHelicalWheel.xml Mon Jun 05 02:44:43 2023 +0000 @@ -0,0 +1,387 @@ +<tool id="edu.tamu.cpt2.helicalWheel.generateHelicalWheel" name="Helical Wheel" version="1.0"> + <description>Generate and Plot a Protein Helical Wheel</description> + <macros> + <import>cpt-macros.xml</import> + <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>