annotate epibuilder-1.1.xml @ 3:0fccf1695099 draft

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author bioinformatics_lab_ufsc
date Thu, 25 Nov 2021 04:24:01 +0000
parents 8fa9e663cca5
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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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bioinformatics_lab_ufsc
parents:
diff changeset
164 </param>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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165 <when value="y" >
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
166 <param name="bepi_out" multiple="false" format="data" type="data" label="File" help="Epitopes predicted by Bepipred 2.0" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
167 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
168 <when value="n" >
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
169 <param name="bepi_out" multiple="false" format="data" type="data" label="File" help="Epitopes predicted by Bepipred 2.0" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
170 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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171 <when value="id" >
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
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" >
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
173 <!-- Check if its an empty value-->
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
174 <validator type="empty_field" message="ID required"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
175 </param>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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176 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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177 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
178 <param name="tresh_bepi2" min="0.0" value="0.6" type="float" label="Threshold for Bepipred 2.0" help="Default = 0.6" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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179 <!-- Epitope Length -->
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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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" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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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" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
182 <!-- EMINI -->
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
183 <conditional name="emini_method">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
184 <param name="emini_choice" type="boolean" checked="true" truevalue="eminiyes" falsevalue="eminino" label="Use Emini Surface Accessibility Prediction method?" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
185 <when value="eminino">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
186 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
187 <when value="eminiyes">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
188 <conditional name="emini_t">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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189 <param name="t_emini" display="radio" type="select" label="Threshold" help="Define threshold for Emini" >
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
190 <option value="d_emini_choice" selected="true">Default (calculated by method)</option>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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191 <option value="t_emini_choice">Set Threshold</option>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
192 </param>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
193 <when value="t_emini_choice">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
194 <param name="thresh_em_value" value="0" type="float" label="Value" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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195 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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196 <when value="d_emini_choice">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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197 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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198 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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199 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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200 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
201 <!-- PARKER -->
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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202 <conditional name="parker_method">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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203 <param name="parker_choice" type="boolean" checked="true" truevalue="parkeryes" falsevalue="parkerno" label="Use Parker Hydrophilicity Prediction method?" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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204 <when value="parkerno">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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205 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
206 <when value="parkeryes">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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207 <conditional name="parker_t">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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208 <param name="t_parker" display="radio" type="select" label="Threshold" help="Define threshold for Parker" >
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
209 <option value="d_parker_choice" selected="true">Default (calculated by method)</option>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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210 <option value="t_parker_choice">Set Threshold</option>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
211 </param>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
212 <when value="t_parker_choice">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
213 <param name="thresh_park_value" value="0" type="float" label="Value" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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214 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
215 <when value="d_parker_choice">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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216 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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217 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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218 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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219 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
220 <!-- Chou -->
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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221 <conditional name="chou_method">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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222 <param name="chou_choice" type="boolean" checked="true" truevalue="chouyes" falsevalue="chouno" label="Use Chou &amp; Fasman Beta-Turn Prediction method?" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
223 <when value="chouno">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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224 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
225 <when value="chouyes">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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226 <conditional name="chou_t">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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227 <param name="t_chou" display="radio" type="select" label="Threshold" help="Define threshold for Chou &amp; Fasman" >
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
228 <option value="d_chou_choice" selected="true">Default (calculated by method)</option>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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229 <option value="t_chou_choice">Set Threshold</option>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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230 </param>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
231 <when value="t_chou_choice">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
232 <param name="thresh_chou_value" value="0" type="float" label="Value" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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233 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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234 <when value="d_chou_choice">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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235 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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236 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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237 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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238 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
239 <!-- Karplus -->
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
240 <conditional name="karplus_method">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
241 <param name="karplus_choice" type="boolean" checked="true" truevalue="karplusyes" falsevalue="karplusno" label="Use Karplus &amp; Schulz Flexibility Prediction method?" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
242 <when value="karplusno">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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243 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
244 <when value="karplusyes">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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245 <conditional name="karplus_t">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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246 <param name="t_karplus" display="radio" type="select" label="Threshold" help="Define threshold for Karplus &amp; Schulz" >
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
247 <option value="d_karplus_choice" selected="true">Default (calculated by method)</option>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
248 <option value="t_karplus_choice">Set Threshold</option>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
249 </param>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
250 <when value="t_karplus_choice">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
251 <param name="thresh_karplus_value" type="float" value="0" label="Value" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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252 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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253 <when value="d_karplus_choice">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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254 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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255 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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256 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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257 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
258 <!-- Kolaskar -->
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
259 <conditional name="kolaskar_method">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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260 <param name="kolaskar_choice" type="boolean" checked="true" truevalue="kolaskaryes" falsevalue="kolaskarno" label="Use Kolaskar &amp; Tongaonkar Antigenicity method?" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
261 <when value="kolaskarno">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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262 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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263 <when value="kolaskaryes">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
264 <conditional name="kolaskar_t">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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265 <param name="t_kolaskar" display="radio" type="select" label="Threshold" help="Define threshold for Kolaskar &amp; Tongaonkar" >
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
266 <option value="d_kolaskar_choice" selected="true">Default (calculated by method)</option>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
267 <option value="t_kolaskar_choice">Set Threshold</option>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
268 </param>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
269 <when value="t_kolaskar_choice">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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270 <param name="thresh_kolaskar_value" type="float" value="0" label="Value" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
271 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
272 <when value="d_kolaskar_choice">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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273 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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274 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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275 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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276 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
277 <!-- Insert Proteome -->
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
278 <conditional name="use_search">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
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?" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
280 <when value="dont">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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281 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
282 <when value="use">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
283 <repeat name="prot_input" title="Proteome" min="1">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
284 <param type="data" name="prot_file" format="fasta" label="Proteome file" help="Protein sequences in fasta format" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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285 <param type="text" name="prot_name" label="Proteome name" help="Give a name to this dataset" >
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
286 <!-- Change spaces for '_' -->
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
287 <sanitizer>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
288 <valid initial="string.printable">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
289 <remove value=" "/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
290 </valid>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
291 <mapping initial="none">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
292 <add source=" " target="_"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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293 </mapping>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
294 </sanitizer>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
295 <!-- Check if its an empty value-->
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
296 <validator type="empty_field" message="Basename required"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
297 </param>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
298 </repeat>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
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" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
300 <conditional name="blast">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
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" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
302 <when value="blastno">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
303 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
304 <when value="blastyes">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
305 <param name="blast_id" value="90" min="1" type="integer" label="Identity" help="[0-100] Minimal identity accepted to parse blast results" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
306 <param name="blast_cover" value="90" min="2" type="integer" label="Coverage" help="[0-100] Minimal coverage accepted to parse blast results" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
307 <param name="blast_wordsize" value="4" min="1" type="integer" label="Word-Size" help="Blast argument word-size" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
308 <param name="blast_task" type="select" label="Task" help="How blastp should run">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
309 <option value="blastp-short" selected="True">Blastp-short</option>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
310 <option value="blastp-fast">Blastp-fast</option>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
311 <option value="blastp">Blastp</option>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
312 </param>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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313 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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314 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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315 </when>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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316 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
317 <param name="basename" type="text" value="" label="Basename" help="Provide a name for this run (string text without special characters)" >
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
318 <!-- Change spaces for '_' -->
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bioinformatics_lab_ufsc
parents:
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319 <sanitizer>
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bioinformatics_lab_ufsc
parents:
diff changeset
320 <valid initial="string.printable">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
321 <remove value=" "/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
322 </valid>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
323 <mapping initial="none">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
324 <add source=" " target="_"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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325 </mapping>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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326 </sanitizer>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
327 <!-- Check if its an empty value-->
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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328 <validator type="empty_field" message="Basename required"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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329 </param>
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bioinformatics_lab_ufsc
parents:
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330 </inputs>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
331 <outputs>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
332 <data name="epif_out" format="txt" from_work_dir="EpiBuilder" label="EpiBuilder Output Summary - ${basename}" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
333 <data name="ep_xls" format="xlsx" from_work_dir="EpiBuilder_report.xlsx" label="EpiBuilder Report - ${basename}" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
334 <collection type="list" label="EpiBuilder Files - ${basename}" name="epif_collection" >
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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335 <discover_datasets format="fasta" pattern="(?P&lt;designation&gt;.*)\.fasta" visible="false" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
336 <discover_datasets format="txt" pattern="(?P&lt;designation&gt;.*)\.tsv" visible="false" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
337 <discover_datasets format="txt" pattern="(?P&lt;designation&gt;.*)\.txt" visible="false" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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338 </collection>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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339 <collection type="list" label="EpiBuilder Blast Run - ${basename}" name="blast_collection" >
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
340 <filter>use_search['search_use_bool'] is True and use_search['blast']['blast_search'] is True</filter>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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341 <discover_datasets pattern="(?P&lt;designation&gt;.*)blast\.csv" visible="false" />
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bioinformatics_lab_ufsc
parents:
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342 </collection>
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bioinformatics_lab_ufsc
parents:
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343 </outputs>
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bioinformatics_lab_ufsc
parents:
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344 <tests>
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bioinformatics_lab_ufsc
parents:
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345 <test>
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bioinformatics_lab_ufsc
parents:
diff changeset
346 <!-- Test all methods threshold selected, command line version of input with proteome-->
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bioinformatics_lab_ufsc
parents:
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347 <conditional name="bepi_type">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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348 <param name="bepipred_origin" value="y"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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349 <param name="bepi_out" value="input_bepi_online.csv"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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350 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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351 <param name="tresh_bepi2" value="0.6"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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352
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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353 <param name="min_length" value="10" />
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bioinformatics_lab_ufsc
parents:
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354 <param name="max_length" value="30" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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355
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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356 <conditional name="emini_method">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
357 <param name="emini_choice" value="eminiyes"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
358 <conditional name="emini_t">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
359 <param name="t_emini" value="t_emini_choice"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
360 <param name="thresh_em_value" value="0.8" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
361 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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362 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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363
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
364 <conditional name="parker_method">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
365 <param name="parker_choice" value="parkeryes"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
366 <conditional name="parker_t">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
367 <param name="t_parker" value="t_parker_choice"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
368 <param name="thresh_park_value" value="0.8" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
369 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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370 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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371
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
372 <conditional name="chou_method">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
373 <param name="chou_choice" value="chouyes"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
374 <conditional name="chou_t">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
375 <param name="t_chou" value="t_chou_choice"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
376 <param name="thresh_chou_value" value="0.8" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
377 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
378 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
379
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
380 <conditional name="karplus_method">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
381 <param name="karplus_choice" value="karplusyes"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
382 <conditional name="karplus_t">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
383 <param name="t_karplus" value="t_karplus_choice"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
384 <param name="thresh_karplus_value" value="0.8" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
385 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
386 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
387
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
388
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
389 <conditional name="kolaskar_method">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
390 <param name="kolaskar_choice" value="kolaskaryes"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
391 <conditional name="kolaskar_t">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
392 <param name="t_kolaskar" value="t_kolaskar_choice"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
393 <param name="thresh_kolaskar_value" value="0.8" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
394 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
395 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
396 <!-- This first part test all methods-->
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
397
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
398 <conditional name="use_search">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
399 <param name="search_use_bool" value="use" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
400 <repeat name="prot_input">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
401 <param name="prot_name" value="test_proteom" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
402 <param name="prot_file" value="proteom.fasta" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
403 </repeat>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
404 <param name="check_use_hit" value="usehit"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
405 <conditional name="blast">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
406 <param name="blast_search" value="blastyes" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
407 <param name="blast_id" value="90" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
408 <param name="blast_cover" value="90" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
409 <param name="blast_wordsize" value="4" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
410 <param name="blast_task" value="blastp-short" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
411 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
412 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
413
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
414 <param name="basename" value="online" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
415
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
416 <output name="epif_out" file="online-EpiBuilder.txt" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
417 <output name="ep_xls" file="online-EpiBuilder.xlsx" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
418 <output_collection name= "epif_collection">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
419 <element name="ep_prot_sum" file="online-EpiBuilder-protein-summary.tsv" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
420 <element name="ep_top" file="online-EpiBuilder-topology.tsv" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
421 <element name="ep_score" file="online-EpiBuilder-socre.tsv" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
422 <element name="ep_detail" file="online-EpiBuilder-epitope-detail.tsv" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
423 <element name="ep_parameters" file="online-EpiBuilder-parameters.tsv" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
424 <element name="ep_fasta" file="online-EpiBuilder-fasta.fasta" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
425 </output_collection>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
426 <output_collection name="blast_collection" >
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
427 <element name="test_proteom" file="online-test_proteom_blast.csv" ftype="csv" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
428 </output_collection >
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
429 </test>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
430
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
431 <test>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
432 <!-- Test all methods threshold selected, online version of input with proteome-->
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
433 <conditional name="bepi_type">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
434 <param name="bepipred_origin" value="y"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
435 <param name="bepi_out" value="input_bcell_command_line.txt"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
436 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
437
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
438 <param name="bepipred_origin" value="n"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
439 <param name="tresh_bepi2" value="0.6"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
440
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
441 <param name="min_length" value="10" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
442 <param name="max_length" value="30" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
443
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
444 <conditional name="emini_method">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
445 <param name="emini_choice" value="eminiyes"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
446 <conditional name="emini_t">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
447 <param name="t_emini" value="t_emini_choice"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
448 <param name="thresh_em_value" value="0.8" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
449 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
450 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
451
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
452 <conditional name="parker_method">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
453 <param name="parker_choice" value="parkeryes"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
454 <conditional name="parker_t">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
455 <param name="t_parker" value="t_parker_choice"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
456 <param name="thresh_park_value" value="0.8" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
457 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
458 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
459
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
460 <conditional name="chou_method">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
461 <param name="chou_choice" value="chouyes"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
462 <conditional name="chou_t">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
463 <param name="t_chou" value="t_chou_choice"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
464 <param name="thresh_chou_value" value="0.8" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
465 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
466 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
467
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
468 <conditional name="karplus_method">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
469 <param name="karplus_choice" value="karplusyes"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
470 <conditional name="karplus_t">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
471 <param name="t_karplus" value="t_karplus_choice"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
472 <param name="thresh_karplus_value" value="0.8" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
473 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
474 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
475
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
476
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
477 <conditional name="kolaskar_method">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
478 <param name="kolaskar_choice" value="kolaskaryes"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
479 <conditional name="kolaskar_t">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
480 <param name="t_kolaskar" value="t_kolaskar_choice"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
481 <param name="thresh_kolaskar_value" value="0.8" />
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bioinformatics_lab_ufsc
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482 </conditional>
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bioinformatics_lab_ufsc
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483 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
484 <!-- This first part test all methods-->
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
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485
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
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486 <conditional name="use_search">
8fa9e663cca5 Uploaded corrected condition for use_hit
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487 <param name="search_use_bool" value="use"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
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488 <repeat name="prot_input">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
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489 <param name="prot_name" value="test_proteom" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
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490 <param name="prot_file" value="proteom.fasta" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
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491 </repeat>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
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492 <param name="check_use_hit" value="usehit"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
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493 <conditional name="blast">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
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494 <param name="blast_search" value="blastyes" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
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495 <param name="blast_id" value="90" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
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496 <param name="blast_cover" value="90"/>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
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497 <param name="blast_wordsize" value="4" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
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498 <param name="blast_task" value="blastp-short" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
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499 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
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500 </conditional>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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501
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
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502 <param name="basename" value="command" />
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bioinformatics_lab_ufsc
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503
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
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504 <output name="epif_out" file="command-EpiBuilder.txt" />
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bioinformatics_lab_ufsc
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diff changeset
505 <output name="ep_xls" file="command-EpiBuilder.xlsx" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
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diff changeset
506 <output_collection name= "epif_collection">
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
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507 <element name="ep_prot_sum" file="command-EpiBuilder-protein-summary.tsv" />
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508 <element name="ep_top" file="command-EpiBuilder-topology.tsv" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
509 <element name="ep_score" file="command-EpiBuilder-socre.tsv" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
510 <element name="ep_detail" file="command-EpiBuilder-epitope-detail.tsv" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
511 <element name="ep_parameters" file="command-EpiBuilder-parameters.tsv" />
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bioinformatics_lab_ufsc
parents:
diff changeset
512 <element name="ep_fasta" file="command-EpiBuilder-fasta.fasta" />
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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513 </output_collection>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
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514 <output_collection name="blast_collection" >
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
515 <element name="test_proteom" file="command-test_proteom_blast.csv" ftype="csv" />
8fa9e663cca5 Uploaded corrected condition for use_hit
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516 </output_collection >
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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517 </test>
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bioinformatics_lab_ufsc
parents:
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518 </tests>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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519 <help>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
520 **How to Run**
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
521
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
522 First, you must have a file with epitopes predicted by Bepipred 2.0 or have one job submmited into bepipred's server.
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
523
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
524 .. class:: warningmark
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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525
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
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526 Input this file (or jobID) and specify if Bepipred 2.0 was ran online or command-line based through bcell standalone suite.
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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527
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
528 Select methods that you want to check your epitopes for validation.
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
529
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
530 Give a threshold for each method (or use default threshold).
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
531
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
532 Optionaly, you can search validated epitopes in proteomes datasets, as many as you wish.
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
533
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
534 .. class:: warningmark
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
535
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
536 If you want to search using Blastp, this software and Makeblastdb must be avaliable on your server's $PATH.
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
537
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
538 -----
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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539
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
540 **Outputs**
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
541
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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542
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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543 **Summary** : Prediction overview
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
544
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
545 **Protein Summary** : Show proteins that have epitopes predicted
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
546
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
547 **Fasta** : Epitopes' sequences
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
548
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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549 **Topology** : Show epitope match in each method, aminoacid per aminoacid
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
550
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
551 **Score** : Detailed score for aminoacids
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
552
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
553 **Epitope Detail** : Properties of each predicted epitope
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
554
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
555 **Parameters** : Softwares, thresholds and parameters used for prediction
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
556
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
557 **Xls Report** : Table with epitope detail, protein summary, topology and scores
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
558
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
559 **Collection with blast files** : All blast results for each proteome
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
560
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
561
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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562 -----
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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563
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
564 .. class:: infomark
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
565
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
566 **For more information, checkout our GitHub page**: https://github.com/bioinfo-ufsc/EpiBuilder
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
567
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
568 -----
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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569
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
570 Please cite methods used in your analysis, available bellow
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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571
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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572 | Bioinformatics Lab - UFSC - 2021
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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573
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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574 </help>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
575 <citations>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
576 <citation type="doi">10.1093/nar/gkx346</citation>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
577 <citation type="doi">10.1016/0014-5793(90)80535-q</citation>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
578 <citation type="doi">10.1002/9780470122921.ch2</citation>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
579 <citation type="doi">10.1021/bi00367a013</citation>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
580 <citation type="doi">https://doi.org/10.1007/BF01195768</citation>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
581 <citation type="doi">doi:10.1128/jvi.55.3.836-839.1985</citation>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
582 <citation type="doi">10.1371/journal.pcbi.1006791</citation>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
583 <citation type="doi">https://doi.org/10.1093/nar/gky379</citation>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
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584 </citations>
8fa9e663cca5 Uploaded corrected condition for use_hit
bioinformatics_lab_ufsc
parents:
diff changeset
585 </tool>