Mercurial > repos > cpt > cpt_helical_wheel

annotate generateHelicalWheel.xml @ 2:e9fb56f44c35 draft default tip

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planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
author cpt
date Fri, 05 Jan 2024 05:52:58 +0000
parents 9b276485c94a
children
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1 <tool id="edu.tamu.cpt2.helicalWheel.generateHelicalWheel" name="Helical Wheel" version="1.0">
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2 <description>Generate and Plot a Protein Helical Wheel</description>
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3 <macros>
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4
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements">
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8 <requirement type="package">numpy</requirement>
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9 <requirement type="package">pandas</requirement>
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10 <requirement type="package" version="0.18.1">scikit-learn</requirement>
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11 <requirement type="package">scipy</requirement>
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12 <requirement type="package">matplotlib</requirement>
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13 </expand>
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14 <command detect_errors="aggressive"><![CDATA[
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15 python '$__tool_directory__/generateHelicalWheel.py'
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16 --sequence '$sequence'
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17 --seqRange '$seqRange'
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18 --t_size '$t_size'
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19 --rotation '$rotation'
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20 '$numbering'
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21 --f_A "$sec_B.f_A"
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22 --f_C "$sec_C.f_C"
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23 --f_D "$sec_D.f_D"
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24 --f_E "$sec_D.f_E"
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25 --f_F "$sec_B.f_F"
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26 --f_G "$sec_C.f_G"
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27 --f_H "$sec_E.f_H"
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28 --f_I "$sec_B.f_I"
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29 --f_K "$sec_E.f_K"
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30 --f_L "$sec_B.f_L"
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31 --f_M "$sec_B.f_M"
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32 --f_N "$sec_C.f_N"
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33 --f_P "$sec_B.f_P"
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34 --f_Q "$sec_C.f_Q"
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35 --f_R "$sec_E.f_R"
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36 --f_S "$sec_C.f_S"
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37 --f_T "$sec_C.f_T"
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38 --f_V "$sec_B.f_V"
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39 --f_W "$sec_B.f_W"
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40 --f_Y "$sec_C.f_Y"
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41 --t_A "$sec_B.t_A"
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42 --t_C "$sec_C.t_C"
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43 --t_D "$sec_D.t_D"
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44 --t_E "$sec_D.t_E"
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45 --t_F "$sec_B.t_F"
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46 --t_G "$sec_C.t_G"
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47 --t_H "$sec_E.t_H"
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48 --t_I "$sec_B.t_I"
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49 --t_K "$sec_E.t_K"
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50 --t_L "$sec_B.t_L"
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51 --t_M "$sec_B.t_M"
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52 --t_N "$sec_C.t_N"
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53 --t_P "$sec_B.t_P"
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54 --t_Q "$sec_C.t_Q"
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55 --t_R "$sec_E.t_R"
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56 --t_S "$sec_C.t_S"
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57 --t_T "$sec_C.t_T"
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58 --t_V "$sec_B.t_V"
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59 --t_W "$sec_B.t_W"
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60 --t_Y "$sec_C.t_Y"
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61 --output '$output'
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62 ]]></command>
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63 <inputs>
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64 <param label="Paste in exact sequence to be plotted" name="sequence" type="text"/>
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65 <param label="Label Start Number" name="seqRange" type="integer" value="1" help="starting residue number to use for labels"/>
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66 <param label="Amino Acid Text Size" name="t_size" type="integer" value="32" help="Alters the Text Size. Default is 32"/>
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67 <param label="Rotation" name="rotation" type="integer" value="90" help="Rotates the helical wheel. Default is 90"/>
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68 <param label="Label Numbering Text" name="numbering" type="boolean" help="number schema subscripts" truevalue="--numbering" falsevalue=""/>
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69 <section name="sec_B" title="nonpolar ; hydrophobic">
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70 <param name="f_A" type="color" label="Color for A" value="#ffcc33">
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71 <sanitizer>
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72 <valid initial="string.ascii_letters,string.digits">
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73 <add value="#"/>
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74 </valid>
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75 </sanitizer>
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76 </param>
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77 <param name="t_A" type="color" label="Text color for A" value="#000000">
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78 <sanitizer>
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79 <valid initial="string.ascii_letters,string.digits">
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80 <add value="#"/>
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81 </valid>
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82 </sanitizer>
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83 </param>
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84 <param name="f_F" type="color" label="Color for F" value="#ffcc33">
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85 <sanitizer>
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86 <valid initial="string.ascii_letters,string.digits">
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87 <add value="#"/>
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88 </valid>
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89 </sanitizer>
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90 </param>
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91 <param name="t_F" type="color" label="Text color for F" value="#000000">
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92 <sanitizer>
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93 <valid initial="string.ascii_letters,string.digits">
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94 <add value="#"/>
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95 </valid>
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96 </sanitizer>
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97 </param>
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98 <param name="f_I" type="color" label="Color for I" value="#ffcc33">
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99 <sanitizer>
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100 <valid initial="string.ascii_letters,string.digits">
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101 <add value="#"/>
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102 </valid>
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103 </sanitizer>
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104 </param>
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105 <param name="t_I" type="color" label="Text color for I" value="#000000">
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106 <sanitizer>
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107 <valid initial="string.ascii_letters,string.digits">
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108 <add value="#"/>
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109 </valid>
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110 </sanitizer>
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111 </param>
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112 <param name="f_L" type="color" label="Color for L" value="#ffcc33">
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113 <sanitizer>
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114 <valid initial="string.ascii_letters,string.digits">
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115 <add value="#"/>
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116 </valid>
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117 </sanitizer>
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118 </param>
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119 <param name="t_L" type="color" label="Text color for L" value="#000000">
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120 <sanitizer>
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121 <valid initial="string.ascii_letters,string.digits">
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122 <add value="#"/>
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123 </valid>
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124 </sanitizer>
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125 </param>
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126 <param name="f_M" type="color" label="Color for M" value="#ffcc33">
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127 <sanitizer>
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128 <valid initial="string.ascii_letters,string.digits">
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129 <add value="#"/>
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130 </valid>
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131 </sanitizer>
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132 </param>
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133 <param name="t_M" type="color" label="Text color for M" value="#000000">
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134 <sanitizer>
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135 <valid initial="string.ascii_letters,string.digits">
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136 <add value="#"/>
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137 </valid>
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138 </sanitizer>
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139 </param>
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140 <param name="f_P" type="color" label="Color for P" value="#ffcc33">
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141 <sanitizer>
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142 <valid initial="string.ascii_letters,string.digits">
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143 <add value="#"/>
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144 </valid>
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145 </sanitizer>
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146 </param>
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147 <param name="t_P" type="color" label="Text color for P" value="#000000">
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148 <sanitizer>
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149 <valid initial="string.ascii_letters,string.digits">
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150 <add value="#"/>
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151 </valid>
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152 </sanitizer>
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153 </param>
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154 <param name="f_V" type="color" label="Color for V" value="#ffcc33">
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155 <sanitizer>
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156 <valid initial="string.ascii_letters,string.digits">
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157 <add value="#"/>
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158 </valid>
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159 </sanitizer>
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160 </param>
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161 <param name="t_V" type="color" label="Text color for V" value="#000000">
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162 <sanitizer>
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163 <valid initial="string.ascii_letters,string.digits">
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164 <add value="#"/>
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165 </valid>
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166 </sanitizer>
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167 </param>
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168 <param name="f_W" type="color" label="Color for W" value="#ffcc33">
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169 <sanitizer>
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170 <valid initial="string.ascii_letters,string.digits">
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171 <add value="#"/>
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172 </valid>
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173 </sanitizer>
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174 </param>
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175 <param name="t_W" type="color" label="Text color for W" value="#000000">
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176 <sanitizer>
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177 <valid initial="string.ascii_letters,string.digits">
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178 <add value="#"/>
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179 </valid>
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180 </sanitizer>
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181 </param>
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182 </section>
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183 <section name="sec_C" title="polar ; uncharged">
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184 <param name="f_C" type="color" label="Color for C" value="#b5b5b5">
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185 <sanitizer>
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186 <valid initial="string.ascii_letters,string.digits">
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187 <add value="#"/>
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188 </valid>
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189 </sanitizer>
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190 </param>
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191 <param name="t_C" type="color" label="Text color for C" value="#000000">
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192 <sanitizer>
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193 <valid initial="string.ascii_letters,string.digits">
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194 <add value="#"/>
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195 </valid>
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196 </sanitizer>
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197 </param>
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198 <param name="f_G" type="color" label="Color for G" value="#b5b5b5">
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199 <sanitizer>
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200 <valid initial="string.ascii_letters,string.digits">
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201 <add value="#"/>
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202 </valid>
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203 </sanitizer>
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204 </param>
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205 <param name="t_G" type="color" label="Text color for G" value="#000000">
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206 <sanitizer>
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207 <valid initial="string.ascii_letters,string.digits">
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208 <add value="#"/>
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209 </valid>
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210 </sanitizer>
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211 </param>
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212 <param name="f_N" type="color" label="Color for N" value="#b5b5b5">
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213 <sanitizer>
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214 <valid initial="string.ascii_letters,string.digits">
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215 <add value="#"/>
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216 </valid>
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217 </sanitizer>
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218 </param>
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219 <param name="t_N" type="color" label="Text color for N" value="#000000">
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220 <sanitizer>
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221 <valid initial="string.ascii_letters,string.digits">
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222 <add value="#"/>
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223 </valid>
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224 </sanitizer>
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225 </param>
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226 <param name="f_Q" type="color" label="Color for Q" value="#b5b5b5">
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227 <sanitizer>
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228 <valid initial="string.ascii_letters,string.digits">
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229 <add value="#"/>
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230 </valid>
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231 </sanitizer>
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232 </param>
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233 <param name="t_Q" type="color" label="Text color for Q" value="#000000">
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234 <sanitizer>
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235 <valid initial="string.ascii_letters,string.digits">
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236 <add value="#"/>
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237 </valid>
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238 </sanitizer>
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239 </param>
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240 <param name="f_S" type="color" label="Color for S" value="#b5b5b5">
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241 <sanitizer>
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242 <valid initial="string.ascii_letters,string.digits">
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243 <add value="#"/>
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244 </valid>
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245 </sanitizer>
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246 </param>
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247 <param name="t_S" type="color" label="Text color for S" value="#000000">
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248 <sanitizer>
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249 <valid initial="string.ascii_letters,string.digits">
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250 <add value="#"/>
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251 </valid>
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252 </sanitizer>
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253 </param>
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254 <param name="f_T" type="color" label="Color for T" value="#b5b5b5">
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255 <sanitizer>
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256 <valid initial="string.ascii_letters,string.digits">
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257 <add value="#"/>
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258 </valid>
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259 </sanitizer>
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260 </param>
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261 <param name="t_T" type="color" label="Text color for T" value="#000000">
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262 <sanitizer>
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263 <valid initial="string.ascii_letters,string.digits">
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264 <add value="#"/>
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265 </valid>
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266 </sanitizer>
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267 </param>
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268 <param name="f_Y" type="color" label="Color for Y" value="#b5b5b5">
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269 <sanitizer>
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270 <valid initial="string.ascii_letters,string.digits">
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271 <add value="#"/>
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272 </valid>
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273 </sanitizer>
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274 </param>
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275 <param name="t_Y" type="color" label="Text color for Y" value="#000000">
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276 <sanitizer>
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277 <valid initial="string.ascii_letters,string.digits">
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278 <add value="#"/>
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279 </valid>
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280 </sanitizer>
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281 </param>
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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282 </section>
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283 <section name="sec_D" title="polar ; acidic (negatively charged)">
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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284 <param name="f_D" type="color" label="Color for D" value="#db270f">
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285 <sanitizer>
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286 <valid initial="string.ascii_letters,string.digits">
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287 <add value="#"/>
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288 </valid>
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289 </sanitizer>
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290 </param>
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291 <param name="t_D" type="color" label="Text color for D" value="#FFFFFF">
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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292 <sanitizer>
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293 <valid initial="string.ascii_letters,string.digits">
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294 <add value="#"/>
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295 </valid>
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296 </sanitizer>
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297 </param>
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298 <param name="f_E" type="color" label="Color for E" value="#db270f">
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299 <sanitizer>
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300 <valid initial="string.ascii_letters,string.digits">
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301 <add value="#"/>
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302 </valid>
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303 </sanitizer>
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304 </param>
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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305 <param name="t_E" type="color" label="Text color for E" value="#FFFFFF">
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306 <sanitizer>
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307 <valid initial="string.ascii_letters,string.digits">
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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308 <add value="#"/>
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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309 </valid>
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310 </sanitizer>
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311 </param>
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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312 </section>
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313 <section name="sec_E" title="polar ; basic (positive charge)">
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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314 <param name="f_H" type="color" label="Color for H" value="#12d5fc">
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315 <sanitizer>
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316 <valid initial="string.ascii_letters,string.digits">
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317 <add value="#"/>
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318 </valid>
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319 </sanitizer>
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320 </param>
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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321 <param name="t_H" type="color" label="Text color for H" value="#000000">
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322 <sanitizer>
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323 <valid initial="string.ascii_letters,string.digits">
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324 <add value="#"/>
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325 </valid>
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326 </sanitizer>
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327 </param>
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328 <param name="f_K" type="color" label="Color for K" value="#12d5fc">
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329 <sanitizer>
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330 <valid initial="string.ascii_letters,string.digits">
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331 <add value="#"/>
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332 </valid>
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333 </sanitizer>
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334 </param>
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335 <param name="t_K" type="color" label="Text color for K" value="#000000">
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336 <sanitizer>
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337 <valid initial="string.ascii_letters,string.digits">
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338 <add value="#"/>
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339 </valid>
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340 </sanitizer>
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341 </param>
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342 <param name="f_R" type="color" label="Color for R" value="#12d5fc">
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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343 <sanitizer>
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344 <valid initial="string.ascii_letters,string.digits">
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345 <add value="#"/>
9b276485c94a planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
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346 </valid>
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347 </sanitizer>
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348 </param>
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349 <param name="t_R" type="color" label="Text color for R" value="#000000">
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350 <sanitizer>
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351 <valid initial="string.ascii_letters,string.digits">
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352 <add value="#"/>
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353 </valid>
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354 </sanitizer>
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355 </param>
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356 </section>
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357 </inputs>
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358 <outputs>
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359 <data format="png" name="output" label="_helicalWheel.png"/>
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360 </outputs>
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361 <help><![CDATA[
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362 **What it does**
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363 INPUT : Peptide Sequence
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364 PARAMETERS :
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365 primary parameters :
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366 > Paste in exact sequence to be plotted - Input Sequence of desired helical wheel plot
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367 > Label Start Number - Numerical value that represents the beginning of the sequence (default 1)
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368 > Amino Acid Text Size - Size of text for helical wheel (default 32)
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369 > Rotation - Degrees to rotate helical wheel (defaul 90)
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370 color parameters :
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371 > Background Color and Text Color Selections
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372 METHOD : Using the core features from the modlAMP python module, a helical wheel projection is constructed.
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373 OUTPUT : _helicalWheel.png
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374 NOTES : Peptide lengths longer than 36 residues will not properly graph.
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375 ]]></help>
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376 <citations>
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377 <citation type="doi">10.1093/bioinformatics/btx285</citation>
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378 <citation type="bibtex">
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379 @unpublished{galaxyTools,
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380 author = {C. Ross},
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381 title = {CPT Galaxy Tools},
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382 year = {2020-},
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383 note = {https://github.com/tamu-cpt/galaxy-tools/}
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384 }
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385 </citation>
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386 </citations>
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387 </tool>