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1 <tool id="anti_ep_pred" name="IEDB BCELL Antibody Epitope Prediction" version="v3.0">
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2 <description>BCELL IEDB Tool</description>
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3 <requirements>
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4 <requirement type="package" version="3.0">IEDB_BCELL</requirement>
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5 <requirement type="package" version="1.0d">Netsurfp</requirement>
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6 <requirement type="package">hh-suite</requirement>
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7 <requirement type="package">MM-seqs2</requirement>
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8 <requirement type="package">nunpy</requirement>
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9 <requirement type="package" version="2.0.0">matplotlib</requirement>
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10 <requirement type="package" version="0.18">scikit-learn</requirement>
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11 <requirement type="package">scipy</requirement>
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12 <requirement type="package" version=">2.7">Python</requirement>
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13 </requirements>
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14 <command interpreter="python">
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15 #if $input_type.choice == "fchoice":
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16 #if $win_size.cutoff != "def":
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17 predict_antibody_epitope.py -m $method -f $input_type.file $png > prediction.txt
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18 #else:
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19 predict_antibody_epitope.py -m $method -f $input_type.file -w $win_size.threshold $png > prediction.txt
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20 #end if
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21 #else:
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22 #if $win_size.cutoff != "def":
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23 predict_antibody_epitope.py -m $method -s $input_type.swissid $png > prediction.txt
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24 #else:
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25 predict_antibody_epitope.py -m $method -s $input_type.swissid -w $win_size.threshold $png > prediction.txt
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26 #end if
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27 #end if
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28 </command>
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29 <inputs>
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30 <conditional name="input_type">
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31 <param name="choice" type="select" display="radio" label="File or Swissprot ID?" >
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32 <option value="fchoice" selected="true">File</option>
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33 <option value="schoice">Swissprot ID</option>
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34 </param>
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35 <when value="fchoice">
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36 <param name="file" type="data" format="fasta" label="Fasta File" help="Fasta or multifasta with protein(s) sequênce(s)" />
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37 </when>
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38 <when value="schoice">
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39 <param name="swissid" type="text" label="SwissprotID"/>
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40 </when>
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41 </conditional>
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42 <param name="method" type="select" display="radio" label="Prediction method">
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43 <option value="Chou-Fasman" selected="true">Chou-Fasman</option>
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44 <option value="Emini">Emini</option>
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45 <option value="Karplus-Schulz">Karplus-Schulz</option>
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46 <option value="Kolaskar-Tongaonkar">Kolaskar-Tongaonkar</option>
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47 <option value="Parker">Parker</option>
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48 <option value="Bepipred">Bepipred</option>
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49 <option value="Bepipred-2.0">Bepipred-2.0</option>
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50 </param>
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51 <conditional name="win_size" >
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52 <param name="cutoff" type="select" display="radio" label="Window Size" >
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53 <option value="" selected="true">Default, defined by method</option>
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54 <option value="def">Set threshold</option>
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55 </param>
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56 <when value="def">
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57 <param name="threshold" type="integer" value="6" label="Threshold"/>
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58 </when>
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59 </conditional>
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60 <param name="png" type="select" display="radio" label="Plot png graph?">
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61 <option value="--plot .">Yes</option>
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62 <option value=" " selected="true">No</option>
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63 </param>
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64 </inputs>
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65 <outputs>
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66 <data name="pred" format="txt" from_work_dir="prediction.txt" label="Antibody Epitope prediction with $method - ${on_string}" />
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67 <data name="png_out" format="png" label="${tool.name} Plot png: ${on_string}" >
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68 <discover_datasets pattern="plot_" ext="png" visible="true" assign_primary_output="true" />
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69 <filter>png == "--plot ."</filter>
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70 </data>
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71 </outputs>
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72 <tests>
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73 <test>
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74 <!-- Testing Chou-Fasman method -->
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75 <param name="method" value="Chou-Fasman" />
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76 <param name="file" value="test/single_sequence.txt" />
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77 <output name="pred" value="test/result_chou.txt" />
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78 <output name="png_out" value="test/png_chou.png" />
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79 </test>
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80 <test>
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81 <!-- Testing Emini method -->
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82 <param name="method" value="Emini" />
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83 <param name="file" value="test/single_sequence.txt" />
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84 <output name="pred" value="test/result_emiini.txt" />
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85 <output name="png_out" value="test/png_emini.png" />
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86 </test>
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87 <test>
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88 <!-- Testing Karplus-Schulz method -->
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89 <param name="method" value="Karplus-Schulz" />
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90 <param name="file" value="test/multiple_sequence.txt" />
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91 <output name="pred" value="test/result_karplus.txt" />
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92 <output name="png_out" value="test/png_karplus.png" />
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93 </test>
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94 <test>
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95 <!-- Testing Kolaskar-Tongaonkar method -->
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96 <param name="method" value="Kolaskar-Tongaonkar" />
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97 <param name="file" value="test/single_sequence.txt" />
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98 <output name="pred" value="test/result_kolaskar.txt" />
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99 <output name="png_out" value="test/png_kolaskar.png" />
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100 </test>
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101 <test>
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102 <!-- Testing Parker method -->
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103 <param name="method" value="Parker" />
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104 <param name="file" value="test/single_sequence.txt" />
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105 <output name="pred" value="test/result_parker.txt" />
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106 <output name="png_out" value="test/png_parker.png" />
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107 </test>
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108 <test>
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109 <!-- Testing Bepipred method -->
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110 <param name="method" value="Bepipred" />
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111 <param name="file" value="test/single_sequence.txt" />
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112 <output name="pred" value="test/result_bepipred1.0.txt" />
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113 <output name="png_out" value="test/png_bepipred1.0.png" />
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114 </test>
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115 <test>
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116 <!-- Testing Bepipred 2.0 method -->
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117 <param name="method" value="Bepipred-2.0" />
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118 <param name="file" value="test/single_sequence.txt" />
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119 <output name="pred" value="test/result_bepipred2.0.txt" />
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120 <output name="png_out" value="test/png_bepipred2.0.png" />
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121 </test>
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122
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123 </tests>
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124
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125 <help>
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126 **How it works**
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127
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128 -----
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129
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130 **This is only bcell interface, need bcell installed on your Galaxy server**
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131
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132 -----
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133
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134 This package contains a collection of methods to predict linear B cell epitopes based on
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135
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136 sequence characteristics of the antigen using amino acid scales and HMMs. The collection
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137
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138 is a mixture of pythons scripts and linux environment specific binaries for Bepipred method.
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139
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140 -----
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141
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142 **WARNING: It's allowed only aminoacid sequences without (*) X and U, please remove it from your sequence before run.**
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143
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144
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145 -----
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146
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147 **Outputs**
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148
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149 - **Antibody Epitope prediction** - Prediction with method and parameters informed;
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150 - **Plot png** - Graphical representation of results;
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151
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152 -----
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153
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154 | We can go on forever with the darkness so far away
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155 | Laboratory of Bioinformatics- UFSC - 2021
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156 </help>
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157 <citations>
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158 <citation type="doi">10.1093/nar/gkx346</citation>
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159 <citation type="doi">10.1110/ps.062405906</citation>
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160 <citation type="doi">10.1186/1472-6807-7-64</citation>
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161 <citation type="doi">10.1186/1745-7580-2-2</citation>
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162 <citation type="doi">10.1021/bi00367a013</citation>
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163 <citation type="doi">10.1016/0014-5793(90)80535-q</citation>
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164 <citation type="doi">10.1002/9780470122921.ch2</citation>
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165 <citation type="bibtex">@ARTICLE{Kim07aninterior-point,
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166 author = {Emini EA, Hughes JV, Perlow DS, Boger J.},
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167 title = {Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide.},
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168 journal = {Journal of virology vol.},
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169 year = {1985 },
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170 volume = {8},
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171 }</citation>
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172 </citations>
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173 </tool>
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