Mercurial > repos > cpt > cpt_fasta_charges

annotate fasta_charges.xml @ 2:defd34aad2dd draft

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author cpt
date Fri, 05 Jan 2024 05:50:48 +0000
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1 <tool id="edu.tamu.cpt.tools.charges" name="Charges" version="2.0">
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2 <description>colour sequences based on rules</description>
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3 <macros>
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4 <import>macros.xml</import>
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5
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 '$__tool_directory__/fasta_charges.py'
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10 '$svg'
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11 @SEQUENCE@
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12
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13 --width '$width'
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14
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15 #if $scheme.cs == "default":
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16 --aa HSQTNCY AVILMPFWG ERDK
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17 --fgColor "#000000" "#000000" "#ffffff"
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18 --bgColor "#ffffff" "#999999" "#000000"
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19 #elif $scheme.cs == "rb":
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20 --aa KR ED HSQTNCYAVILMPFWG
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21 --fgColor "#ffffff" "#ffffff" "#000000"
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22 --bgColor "#00b0f0" "#fc0000" "#ffffff"
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23 #elif $scheme.cs == "rbgb":
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24 --aa KR ED P C HSQTNYAVILMFWG
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25 --fgColor "#ffffff" "#ffffff" "#ffffff" "#ffffff" "#000000"
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26 --bgColor "#00b0f0" "#fc0000" "#1cb026" "#805839" "#ffffff"
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27 #else:
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28 --aa
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29 #for group in '$scheme.groups':
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30 "$group.aminoAcids"
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31 #end for
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32 --fgColor
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33 #for group in '$scheme.groups':
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34 "$group.fgColour"
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35 #end for
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36 --bgColor
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37 #for group in '$scheme.groups':
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38 "$group.bgColour"
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39 #end for
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40 #end if
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41
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42 > $html ]]>
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43 </command>
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44 <inputs>
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45 <expand macro="input/fasta/protein"/>
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46 <param label="Output format" name="svg" type="select">
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47 <option value="">HTML</option>
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48 <option value="--svg">SVG</option>
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49 </param>
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50 <conditional name="scheme">
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51 <param label="Colour scheme" name="cs" type="select">
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52 <option value="default">Default hyrophobic/polar/charged</option>
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53 <option value="rb">Positives Blue, Negatives Red</option>
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54 <option value="rbgb">Positives Blue, Negatives Red, Prolines Green, Cysteines Brown</option>
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55 <option value="custom">Custom Colour Scheme</option>
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56 </param>
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57 <when value="default"/>
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58 <when value="rb"/>
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59 <when value="custom">
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60 <repeat name="groups" title="Colour Group">
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61 <param name="aminoAcids" type="text" label="Amino Acids" help="Amino acids to colour a specific colour"/>
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62 <param name="fgColour" type="color" label="Foreground Color"/>
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63 <param name="bgColour" type="color" label="Background Color"/>
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64 </repeat>
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65 </when>
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66 </conditional>
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67 <param label="Plot width" name="width" type="integer" value="120"/>
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68 </inputs>
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69 <outputs>
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70 <data format="html" name="html">
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71 <change_format>
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72 <when input="svg" value="--svg" format="svg"/>
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73 </change_format>
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74 </data>
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75 </outputs>
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76 <tests>
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77 <test>
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78 <param name="sequences" value="prot.fa"/>
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79 <param name="cs" value="default"/>
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80 <param name="width" value="120"/>
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81 <output name="html" file="charges.html"/>
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82 </test>
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83 </tests>
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84 <help>
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85 **What it does**
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86
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87 Colors fasta (protein) sequences based on rules, and displays outputs as HTML.
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88 </help>
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89 <expand macro="citations"/>
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90 </tool>