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1 <tool id="epibuilder_1.1" name="EpiBuilder" version="1.1">
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2 <description>Predict B cell epitopes</description>
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3 <requirements>
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4 <requirement type="package" version=">=1.8">Java</requirement>
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5 <requirement type="package" version=">=2.11.0+">Blastp</requirement>
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6 <requirement type="package" version=">=2.11.0+">Makeblastdb</requirement>
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7 </requirements>
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8 <stdio>
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9 <regex match="command not found"
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10 source="both"
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11 level="log"
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12 description="WARNING: some methods could not be applied -> check inputs and outputs files" />
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13 <regex match="makeblastdb "
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14 source="both"
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15 level="log"
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16 description="makeblastdb and blastp must be in $PATH on your Galaxy server" />
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17 <regex match="blastp "
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18 source="both"
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19 level="log"
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20 description="makeblastdb and blastp must be in $PATH on your Galaxy server" />
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21 </stdio>
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22 <command><![CDATA[
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23 #*<!--
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24 Methods used will be saved in $param with each threshold
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25 Threshold is separated from method by ":"
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26 Each method is separated by ";"
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27 example: emini:0.8;parker:d;
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28
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29 >> d means defalt threshold
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30 -->*#
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31
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32 #*<!-- Set variables that concatenate methods -->*#
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33 #set param = ''
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34 #set nomethod = ''
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35 #set proteomes = ''
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36
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37 #*<!-- Add Bepipred2.0 method -->*#
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38 #if $bepi_type.bepipred_origin == 'y':
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39 #set bepipred_origin = '-o'
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40 #*<!-- jobid -->*#
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41 #elif $bepi_type.bepipred_origin == 'id':
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42 #set bepipred_origin = '-jobid ' + str($bepi_type.job_id)
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43 #else:
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44 #set bepipred_origin = ''
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45 #end if
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46
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47 #*<!-- Add Emini method -->*#
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48 #if $emini_method.emini_choice == 'eminiyes':
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49 #if $emini_method.emini_t.t_emini == 't_emini_choice'
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50 #set param += 'emini:' + str($emini_method.emini_t.thresh_em_value) + ';'
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51 #else:
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52 #set param += 'emini:d;'
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53 #end if
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54 #end if
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55
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56 #*<!-- Add Parker method -->*#
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57 #if $parker_method.parker_choice == 'parkeryes':
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58 #if $parker_method.parker_t.t_parker == 't_parker_choice'
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59 #set param += 'parker:' + str($parker_method.parker_t.thresh_park_value) + ';'
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60 #else:
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61 #set param += 'parker:d;'
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62 #end if
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63 #end if
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64
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65 #*<!-- Add Chou method -->*#
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66 #if $chou_method.chou_choice == 'chouyes':
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67 #if $chou_method.chou_t.t_chou == 't_chou_choice'
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68 #set param += 'chou_fosman:' + str($chou_method.chou_t.thresh_chou_value) + ';'
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69 #else:
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70 #set param += 'chou_fosman:d;'
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71 #end if
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72 #end if
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73
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74 #*<!-- Add Karplus method -->*#
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75 #if $karplus_method.karplus_choice == 'karplusyes':
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76 #if $karplus_method.karplus_t.t_karplus == 't_karplus_choice'
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77 #set param += 'karplus_schulz:' + str($karplus_method.karplus_t.thresh_karplus_value) + ';'
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78 #else:
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79 #set param += 'karplus_schulz:d;'
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80 #end if
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81 #end if
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82
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83 #*<!-- Add Kolaskar method -->*#
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84 #if $kolaskar_method.kolaskar_choice == 'kolaskaryes':
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85 #if $kolaskar_method.kolaskar_t.t_kolaskar == 't_kolaskar_choice'
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86 #set param += 'kolaskar:' + str($kolaskar_method.kolaskar_t.thresh_kolaskar_value) + ';'
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87 #else:
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88 #set param += 'kolaskar:d;'
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89 #end if
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90 #end if
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91
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92
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93
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94 #*<!-- Clean $proteome if there's no protome -->*#
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95 #if proteomes == '-proteomes ':
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96 #set proteomes = ''
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97 #end if
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98
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99
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100 #*<!-- Parse blast command -->*#
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101
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102 #if $use_search.search_use_bool == "use":
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103 #*<!-- Add proteomes, as many as given -->*#
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104 #if $use_search.prot_input:
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105 #for $file in $use_search.prot_input:
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106 #set proteomes += str($file.prot_name) + '=' + str($file.prot_file) + ';'
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107 #end for
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108 #end if
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109 #if $use_search.prot_input:
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110 #if $use_search.blast.blast_search == 'blastyes':
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111 #set blast_command = 'task=' + str($use_search.blast.blast_task)
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112 #set blast_command += ';identity=' + str($use_search.blast.blast_id) + ';cover=' + str($use_search.blast.blast_cover) + ';word-size=' + str($use_search.blast.blast_wordsize)
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113 #set blast_command += ';makeblastdb_path=makeblastdb;blastp_path=blastp'
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114 #end if
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115 #end if
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116 #end if
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117
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118 #*<!-- Paste Command-line and run -->*#
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119
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120 java -jar $__tool_directory__/epibuilder-1.1.jar
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121
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122 #*<!-- bepipred_origin give -o if online, nothing if command and -jobid if jobID -->*#
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123 #*<!-- if origin is not jobid, there is a file, and -b must be passed -->*#
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124 #if $bepi_type.bepipred_origin != 'id':
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125 -b ${bepi_type.bepi_out}
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126 #end if
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127 -t ${tresh_bepi2}
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128 ${bepipred_origin}
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129 #if $param:
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130 -p "${param}"
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131 #end if
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132 -f "${basename}"
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133 -min_len ${min_length}
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134 -max_len ${max_length}
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135 #if $proteomes:
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136 -proteomes
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137 "${proteomes}"
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138 #if $use_search.blast.blast_search == 'blastyes':
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139 -blast "${blast_command}"
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140 #end if
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141 #end if
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142
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143 #if $use_search.check_use_hit == 'nousehit':
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144 -nohitacc
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145 #end if
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146 #*<!-- DONT REMOVE THIS ; -->*#
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147 >log.log 2>log.log;
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148
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149 mv $basename-epibuilder.xlsx EpiBuilder_report.xlsx;
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150
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151 #*<!-- Rename output files -->*#
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152 mv ${basename}-epibuilder.txt EpiBuilder;
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153
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154
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155 ]]>
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156 </command>
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157 <inputs>
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158 <!-- Bepipred 2.0 -->
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159 <conditional name="bepi_type">
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160 <param name="bepipred_origin" type="select" display="radio" label="Input files" help="Online prediction returns a csv file, command-line based returns a tsv file" >
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161 <option value="y" selected="true">csv file from Bepipred 2.0</option>
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162 <option value="n" >text file from IEDB Bcell Software standalone</option>
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163 <option value="id">JobID from Bepipred 2.0 Server</option>
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164 </param>
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165 <when value="y" >
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166 <param name="bepi_out" multiple="false" format="data" type="data" label="File" help="Epitopes predicted by Bepipred 2.0" />
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167 </when>
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168 <when value="n" >
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169 <param name="bepi_out" multiple="false" format="data" type="data" label="File" help="Epitopes predicted by Bepipred 2.0" />
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170 </when>
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171 <when value="id" >
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172 <param name="job_id" type="text" value="" label="JobID" help="Prediction must be complete - check it in: http://www.cbs.dtu.dk/cgi-bin/webface2.fcgi?jobid=YOUR_JOB_ID" >
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173 <!-- Check if its an empty value-->
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174 <validator type="empty_field" message="ID required"/>
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175 </param>
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176 </when>
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177 </conditional>
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178 <param name="tresh_bepi2" min="0.0" value="0.6" type="float" label="Threshold for Bepipred 2.0" help="Default = 0.6" />
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179 <!-- Epitope Length -->
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180 <param name="min_length" value="10" min="1" type="integer" label="Min epitope length" help="[1-X] Minimal length must be smaller than maximal length" />
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181 <param name="max_length" value="30" min="2" type="integer" label="Max epitope length" help="[2-X] Maximal length must be greather than minimal length" />
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182 <!-- EMINI -->
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183 <conditional name="emini_method">
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184 <param name="emini_choice" type="boolean" checked="true" truevalue="eminiyes" falsevalue="eminino" label="Use Emini Surface Accessibility Prediction method?" />
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185 <when value="eminino">
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186 </when>
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187 <when value="eminiyes">
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188 <conditional name="emini_t">
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189 <param name="t_emini" display="radio" type="select" label="Threshold" help="Define threshold for Emini" >
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190 <option value="d_emini_choice" selected="true">Default (calculated by method)</option>
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191 <option value="t_emini_choice">Set Threshold</option>
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192 </param>
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193 <when value="t_emini_choice">
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194 <param name="thresh_em_value" value="0" type="float" label="Value" />
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195 </when>
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196 <when value="d_emini_choice">
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197 </when>
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198 </conditional>
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199 </when>
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200 </conditional>
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201 <!-- PARKER -->
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202 <conditional name="parker_method">
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203 <param name="parker_choice" type="boolean" checked="true" truevalue="parkeryes" falsevalue="parkerno" label="Use Parker Hydrophilicity Prediction method?" />
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204 <when value="parkerno">
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205 </when>
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206 <when value="parkeryes">
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207 <conditional name="parker_t">
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208 <param name="t_parker" display="radio" type="select" label="Threshold" help="Define threshold for Parker" >
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209 <option value="d_parker_choice" selected="true">Default (calculated by method)</option>
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210 <option value="t_parker_choice">Set Threshold</option>
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211 </param>
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212 <when value="t_parker_choice">
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213 <param name="thresh_park_value" value="0" type="float" label="Value" />
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214 </when>
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215 <when value="d_parker_choice">
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216 </when>
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217 </conditional>
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218 </when>
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219 </conditional>
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220 <!-- Chou -->
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221 <conditional name="chou_method">
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222 <param name="chou_choice" type="boolean" checked="true" truevalue="chouyes" falsevalue="chouno" label="Use Chou & Fasman Beta-Turn Prediction method?" />
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223 <when value="chouno">
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224 </when>
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225 <when value="chouyes">
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226 <conditional name="chou_t">
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227 <param name="t_chou" display="radio" type="select" label="Threshold" help="Define threshold for Chou & Fasman" >
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228 <option value="d_chou_choice" selected="true">Default (calculated by method)</option>
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229 <option value="t_chou_choice">Set Threshold</option>
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230 </param>
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231 <when value="t_chou_choice">
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232 <param name="thresh_chou_value" value="0" type="float" label="Value" />
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233 </when>
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234 <when value="d_chou_choice">
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235 </when>
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236 </conditional>
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237 </when>
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238 </conditional>
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239 <!-- Karplus -->
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240 <conditional name="karplus_method">
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241 <param name="karplus_choice" type="boolean" checked="true" truevalue="karplusyes" falsevalue="karplusno" label="Use Karplus & Schulz Flexibility Prediction method?" />
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242 <when value="karplusno">
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243 </when>
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244 <when value="karplusyes">
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245 <conditional name="karplus_t">
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246 <param name="t_karplus" display="radio" type="select" label="Threshold" help="Define threshold for Karplus & Schulz" >
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247 <option value="d_karplus_choice" selected="true">Default (calculated by method)</option>
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248 <option value="t_karplus_choice">Set Threshold</option>
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249 </param>
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250 <when value="t_karplus_choice">
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251 <param name="thresh_karplus_value" type="float" value="0" label="Value" />
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252 </when>
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253 <when value="d_karplus_choice">
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254 </when>
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255 </conditional>
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256 </when>
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257 </conditional>
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258 <!-- Kolaskar -->
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259 <conditional name="kolaskar_method">
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260 <param name="kolaskar_choice" type="boolean" checked="true" truevalue="kolaskaryes" falsevalue="kolaskarno" label="Use Kolaskar & Tongaonkar Antigenicity method?" />
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261 <when value="kolaskarno">
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262 </when>
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263 <when value="kolaskaryes">
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264 <conditional name="kolaskar_t">
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265 <param name="t_kolaskar" display="radio" type="select" label="Threshold" help="Define threshold for Kolaskar & Tongaonkar" >
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266 <option value="d_kolaskar_choice" selected="true">Default (calculated by method)</option>
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267 <option value="t_kolaskar_choice">Set Threshold</option>
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268 </param>
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269 <when value="t_kolaskar_choice">
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270 <param name="thresh_kolaskar_value" type="float" value="0" label="Value" />
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271 </when>
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272 <when value="d_kolaskar_choice">
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273 </when>
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274 </conditional>
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275 </when>
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276 </conditional>
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277 <!-- Insert Proteome -->
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278 <conditional name="use_search">
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279 <param name="search_use_bool" type="boolean" checked="false" truevalue="use" falsevalue="dont" label="Do you want to search the predicted epitopes in a proteome file?" />
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280 <when value="dont">
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281 </when>
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282 <when value="use">
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283 <repeat name="prot_input" title="Proteome" min="1">
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284 <param type="data" name="prot_file" format="fasta" label="Proteome file" help="Protein sequences in fasta format" />
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285 <param type="text" name="prot_name" label="Proteome name" help="Give a name to this dataset" >
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286 <!-- Change spaces for '_' -->
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287 <sanitizer>
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288 <valid initial="string.printable">
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289 <remove value=" "/>
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290 </valid>
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291 <mapping initial="none">
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292 <add source=" " target="_"/>
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293 </mapping>
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294 </sanitizer>
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295 <!-- Check if its an empty value-->
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296 <validator type="empty_field" message="Basename required"/>
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297 </param>
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298 </repeat>
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299 <param name="check_use_hit" type="boolean" checked="true" truevalue="usehit" falsevalue="nousehit" label="Show accession ID on result files?" help="Choose this option if you want to add accession ID numbers" />
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300 <conditional name="blast">
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301 <param name="blast_search" type="boolean" checked="false" truevalue="blastyes" falsevalue="blastno" label="Blastp" help="Choose this option if you want to add a blast search for epitopes in proteomes" />
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302 <when value="blastno">
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303 </when>
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304 <when value="blastyes">
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305 <param name="blast_id" value="90" min="1" type="integer" label="Identity" help="[0-100] Minimal identity accepted to parse blast results" />
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306 <param name="blast_cover" value="90" min="2" type="integer" label="Coverage" help="[0-100] Minimal coverage accepted to parse blast results" />
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307 <param name="blast_wordsize" value="4" min="1" type="integer" label="Word-Size" help="Blast argument word-size" />
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308 <param name="blast_task" type="select" label="Task" help="How blastp should run">
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309 <option value="blastp-short" selected="True">Blastp-short</option>
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310 <option value="blastp-fast">Blastp-fast</option>
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311 <option value="blastp">Blastp</option>
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312 </param>
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313 </when>
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314 </conditional>
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315 </when>
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316 </conditional>
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317 <param name="basename" type="text" value="" label="Basename" help="Provide a name for this run (string text without special characters)" >
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318 <!-- Change spaces for '_' -->
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319 <sanitizer>
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320 <valid initial="string.printable">
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321 <remove value=" "/>
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322 </valid>
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323 <mapping initial="none">
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324 <add source=" " target="_"/>
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325 </mapping>
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326 </sanitizer>
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327 <!-- Check if its an empty value-->
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328 <validator type="empty_field" message="Basename required"/>
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329 </param>
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330 </inputs>
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331 <outputs>
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332 <data name="epif_out" format="txt" from_work_dir="EpiBuilder" label="EpiBuilder Output Summary - ${basename}" />
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333 <data name="ep_xls" format="xlsx" from_work_dir="EpiBuilder_report.xlsx" label="EpiBuilder Report - ${basename}" />
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334 <collection type="list" label="EpiBuilder Files - ${basename}" name="epif_collection" >
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335 <discover_datasets format="fasta" pattern="(?P<designation>.*)\.fasta" visible="false" />
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336 <discover_datasets format="txt" pattern="(?P<designation>.*)\.tsv" visible="false" />
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337 <discover_datasets format="txt" pattern="(?P<designation>.*)\.txt" visible="false" />
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338 </collection>
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339 <collection type="list" label="EpiBuilder Blast Run - ${basename}" name="blast_collection" >
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340 <filter>use_search['search_use_bool'] is True and use_search['blast']['blast_search'] is True</filter>
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341 <discover_datasets pattern="(?P<designation>.*)blast\.csv" visible="false" />
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342 </collection>
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343 </outputs>
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344 <tests>
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345 <test>
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346 <!-- Test all methods threshold selected, command line version of input with proteome-->
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347 <conditional name="bepi_type">
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348 <param name="bepipred_origin" value="y"/>
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349 <param name="bepi_out" value="input_bepi_online.csv"/>
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350 </conditional>
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351 <param name="tresh_bepi2" value="0.6"/>
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352
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353 <param name="min_length" value="10" />
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354 <param name="max_length" value="30" />
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355
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356 <conditional name="emini_method">
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357 <param name="emini_choice" value="eminiyes"/>
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358 <conditional name="emini_t">
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359 <param name="t_emini" value="t_emini_choice"/>
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360 <param name="thresh_em_value" value="0.8" />
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361 </conditional>
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362 </conditional>
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363
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364 <conditional name="parker_method">
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365 <param name="parker_choice" value="parkeryes"/>
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366 <conditional name="parker_t">
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367 <param name="t_parker" value="t_parker_choice"/>
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368 <param name="thresh_park_value" value="0.8" />
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369 </conditional>
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370 </conditional>
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371
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372 <conditional name="chou_method">
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373 <param name="chou_choice" value="chouyes"/>
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374 <conditional name="chou_t">
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375 <param name="t_chou" value="t_chou_choice"/>
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376 <param name="thresh_chou_value" value="0.8" />
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377 </conditional>
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378 </conditional>
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379
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380 <conditional name="karplus_method">
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381 <param name="karplus_choice" value="karplusyes"/>
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382 <conditional name="karplus_t">
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383 <param name="t_karplus" value="t_karplus_choice"/>
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384 <param name="thresh_karplus_value" value="0.8" />
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385 </conditional>
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386 </conditional>
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387
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388
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389 <conditional name="kolaskar_method">
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390 <param name="kolaskar_choice" value="kolaskaryes"/>
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391 <conditional name="kolaskar_t">
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392 <param name="t_kolaskar" value="t_kolaskar_choice"/>
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393 <param name="thresh_kolaskar_value" value="0.8" />
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394 </conditional>
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395 </conditional>
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396 <!-- This first part test all methods-->
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397
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398 <conditional name="use_search">
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399 <param name="search_use_bool" value="use" />
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400 <repeat name="prot_input">
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401 <param name="prot_name" value="test_proteom" />
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402 <param name="prot_file" value="proteom.fasta" />
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403 </repeat>
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404 <conditional name="check_use_hit" value="usehit"/>
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405 <conditional name="blast">
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406 <param name="blast_search" value="blastyes" />
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407 <param name="blast_id" value="90" />
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408 <param name="blast_cover" value="90" />
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409 <param name="blast_wordsize" value="4" />
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410 <param name="blast_task" value="blastp-short" />
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411 </conditional>
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412 </conditional>
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413
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414 <param name="basename" value="online" />
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415
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416 <output name="epif_out" file="online-EpiBuilder.txt" />
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417 <output name="ep_xls" file="online-EpiBuilder.xlsx" />
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418 <output_collection name= "epif_collection">
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419 <element name="ep_prot_sum" file="online-EpiBuilder-protein-summary.tsv" />
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420 <element name="ep_top" file="online-EpiBuilder-topology.tsv" />
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421 <element name="ep_score" file="online-EpiBuilder-socre.tsv" />
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422 <element name="ep_detail" file="online-EpiBuilder-epitope-detail.tsv" />
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423 <element name="ep_parameters" file="online-EpiBuilder-parameters.tsv" />
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424 <element name="ep_fasta" file="online-EpiBuilder-fasta.fasta" />
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425 </output_collection>
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426 <output_collection name="blast_collection" >
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427 <element name="test_proteom" file="online-test_proteom_blast.csv" ftype="csv" />
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428 </output_collection >
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429 </test>
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430
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431 <test>
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432 <!-- Test all methods threshold selected, online version of input with proteome-->
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433 <conditional name="bepi_type">
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434 <param name="bepipred_origin" value="y"/>
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435 <param name="bepi_out" value="input_bcell_command_line.txt"/>
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436 </conditional>
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437
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438 <param name="bepipred_origin" value="n"/>
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439 <param name="tresh_bepi2" value="0.6"/>
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440
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441 <param name="min_length" value="10" />
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442 <param name="max_length" value="30" />
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443
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444 <conditional name="emini_method">
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445 <param name="emini_choice" value="eminiyes"/>
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446 <conditional name="emini_t">
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447 <param name="t_emini" value="t_emini_choice"/>
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448 <param name="thresh_em_value" value="0.8" />
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449 </conditional>
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450 </conditional>
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451
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452 <conditional name="parker_method">
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453 <param name="parker_choice" value="parkeryes"/>
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454 <conditional name="parker_t">
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455 <param name="t_parker" value="t_parker_choice"/>
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456 <param name="thresh_park_value" value="0.8" />
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457 </conditional>
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458 </conditional>
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459
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460 <conditional name="chou_method">
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461 <param name="chou_choice" value="chouyes"/>
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462 <conditional name="chou_t">
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463 <param name="t_chou" value="t_chou_choice"/>
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464 <param name="thresh_chou_value" value="0.8" />
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465 </conditional>
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466 </conditional>
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467
|
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468 <conditional name="karplus_method">
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469 <param name="karplus_choice" value="karplusyes"/>
|
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470 <conditional name="karplus_t">
|
|
|
471 <param name="t_karplus" value="t_karplus_choice"/>
|
|
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472 <param name="thresh_karplus_value" value="0.8" />
|
|
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473 </conditional>
|
|
|
474 </conditional>
|
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475
|
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476
|
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477 <conditional name="kolaskar_method">
|
|
|
478 <param name="kolaskar_choice" value="kolaskaryes"/>
|
|
|
479 <conditional name="kolaskar_t">
|
|
|
480 <param name="t_kolaskar" value="t_kolaskar_choice"/>
|
|
|
481 <param name="thresh_kolaskar_value" value="0.8" />
|
|
|
482 </conditional>
|
|
|
483 </conditional>
|
|
|
484 <!-- This first part test all methods-->
|
|
|
485
|
|
|
486 <conditional name="use_search">
|
|
|
487 <param name="search_use_bool" value="use"/>
|
|
|
488 <repeat name="prot_input">
|
|
|
489 <param name="prot_name" value="test_proteom" />
|
|
|
490 <param name="prot_file" value="proteom.fasta" />
|
|
|
491 </repeat>
|
|
|
492 <conditional name="check_use_hit" value="usehit"/>
|
|
|
493 <conditional name="blast">
|
|
|
494 <param name="blast_search" value="blastyes" />
|
|
|
495 <param name="blast_id" value="90" />
|
|
|
496 <param name="blast_cover" value="90"/>
|
|
|
497 <param name="blast_wordsize" value="4" />
|
|
|
498 <param name="blast_task" value="blastp-short" />
|
|
|
499 </conditional>
|
|
|
500 </conditional>
|
|
|
501
|
|
|
502 <param name="basename" value="command" />
|
|
|
503
|
|
|
504 <output name="epif_out" file="command-EpiBuilder.txt" />
|
|
|
505 <output name="ep_xls" file="command-EpiBuilder.xlsx" />
|
|
|
506 <output_collection name= "epif_collection">
|
|
|
507 <element name="ep_prot_sum" file="command-EpiBuilder-protein-summary.tsv" />
|
|
|
508 <element name="ep_top" file="command-EpiBuilder-topology.tsv" />
|
|
|
509 <element name="ep_score" file="command-EpiBuilder-socre.tsv" />
|
|
|
510 <element name="ep_detail" file="command-EpiBuilder-epitope-detail.tsv" />
|
|
|
511 <element name="ep_parameters" file="command-EpiBuilder-parameters.tsv" />
|
|
|
512 <element name="ep_fasta" file="command-EpiBuilder-fasta.fasta" />
|
|
|
513 </output_collection>
|
|
|
514 <output_collection name="blast_collection" >
|
|
|
515 <element name="test_proteom" file="command-test_proteom_blast.csv" ftype="csv" />
|
|
|
516 </output_collection >
|
|
|
517 </test>
|
|
|
518 </tests>
|
|
|
519 <help>
|
|
|
520 **How to Run**
|
|
|
521
|
|
|
522 First, you must have a file with epitopes predicted by Bepipred 2.0 or have one job submmited into bepipred's server.
|
|
|
523
|
|
|
524 .. class:: warningmark
|
|
|
525
|
|
|
526 Input this file (or jobID) and specify if Bepipred 2.0 was ran online or command-line based through bcell standalone suite.
|
|
|
527
|
|
|
528 Select methods that you want to check your epitopes for validation.
|
|
|
529
|
|
|
530 Give a threshold for each method (or use default threshold).
|
|
|
531
|
|
|
532 Optionaly, you can search validated epitopes in proteomes datasets, as many as you wish.
|
|
|
533
|
|
|
534 .. class:: warningmark
|
|
|
535
|
|
|
536 If you want to search using Blastp, this software and Makeblastdb must be avaliable on your server's $PATH.
|
|
|
537
|
|
|
538 -----
|
|
|
539
|
|
|
540 **Outputs**
|
|
|
541
|
|
|
542
|
|
|
543 **Summary** : Prediction overview
|
|
|
544
|
|
|
545 **Protein Summary** : Show proteins that have epitopes predicted
|
|
|
546
|
|
|
547 **Fasta** : Epitopes' sequences
|
|
|
548
|
|
|
549 **Topology** : Show epitope match in each method, aminoacid per aminoacid
|
|
|
550
|
|
|
551 **Score** : Detailed score for aminoacids
|
|
|
552
|
|
|
553 **Epitope Detail** : Properties of each predicted epitope
|
|
|
554
|
|
|
555 **Parameters** : Softwares, thresholds and parameters used for prediction
|
|
|
556
|
|
|
557 **Xls Report** : Table with epitope detail, protein summary, topology and scores
|
|
|
558
|
|
|
559 **Collection with blast files** : All blast results for each proteome
|
|
|
560
|
|
|
561
|
|
|
562 -----
|
|
|
563
|
|
|
564 .. class:: infomark
|
|
|
565
|
|
|
566 **For more information, checkout our GitHub page**: https://github.com/bioinfo-ufsc/EpiBuilder
|
|
|
567
|
|
|
568 -----
|
|
|
569
|
|
|
570 Please cite methods used in your analysis, available bellow
|
|
|
571
|
|
|
572 | Bioinformatics Lab - UFSC - 2021
|
|
|
573
|
|
|
574 </help>
|
|
|
575 <citations>
|
|
|
576 <citation type="doi">10.1093/nar/gkx346</citation>
|
|
|
577 <citation type="doi">10.1016/0014-5793(90)80535-q</citation>
|
|
|
578 <citation type="doi">10.1002/9780470122921.ch2</citation>
|
|
|
579 <citation type="doi">10.1021/bi00367a013</citation>
|
|
|
580 <citation type="doi">https://doi.org/10.1007/BF01195768</citation>
|
|
|
581 <citation type="doi">doi:10.1128/jvi.55.3.836-839.1985</citation>
|
|
|
582 <citation type="doi">10.1371/journal.pcbi.1006791</citation>
|
|
|
583 <citation type="doi">https://doi.org/10.1093/nar/gky379</citation>
|
|
|
584 </citations>
|
|
|
585 </tool>
|
|
|
586
|
