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1 <tool id="iedb_api" name="IEDB" version="0.1.0">
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2 <description>MHC Binding prediction</description>
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3 <requirements>
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4 </requirements>
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5 <stdio>
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6 <exit_code range="1:" />
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7 </stdio>
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8 <command interpreter="python"><![CDATA[
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9 #import re
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10 iedb_api.py --prediction=$prediction.tool --method=$prediction.method
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11 #if $sequence.seqsrc == 'fasta':
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12 -i $sequence.seq_fasta
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13 #else if $sequence.seqsrc == 'tabular':
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14 -i $sequence.seq_tsv
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15 -c #echo int(str($sequence.pep_col)) - 1
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16 #if $sequence.id_col:
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17 -C #echo int(str($sequence.id_col)) - 1
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18 #end if
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19 #else:
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20 #for $seq in str($sequence.seq_text).strip().split():
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21 -s $seq.strip()
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22 #end for
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23 #end if
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24 #if $alleles.allelesrc == 'history':
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25 #for $line in open(str($alleles.allele_file)):
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26 #set $fields = $line.strip().split(',')
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27 #set $allele = $fields[0].strip()
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28 #if len($allele) > 0:
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29 #if len($fields) > 1:
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30 #for $alen in $fields[1:]:
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31 -a $allele -l $alen
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32 #end for
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33 #else:
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34 #for $alen in str($lengths).split(','):
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35 -a $allele -l $alen
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36 #end for
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37 #end if
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38 #end if
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39 #end for
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40 #else:
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41 #for $word in str($alleles.allele_text).strip().split():
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42 #set $fields = $word.strip().split(',')
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43 #set $allele = $fields[0].strip()
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44 #if len($allele) > 0:
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45 #if len($fields) > 1:
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46 #for $alen in $fields[1:]:
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47 -a $allele -l $alen
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48 #end for
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49 #else:
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50 #for $alen in str($lengths).split(','):
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51 -a $allele -l $alen
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52 #end for
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53 #end if
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54 #end if
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55 #end for
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56 #end if
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57 -o $output
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58 ]]></command>
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59 <inputs>
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60 <conditional name="sequence">
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61 <param name="seqsrc" type="select" label="Peptide sequences">
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62 <option value="fasta">Fasta file</option>
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63 <option value="tabular">From tabular</option>
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64 <option value="entry"></option>
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65 </param>
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66 <when value="fasta">
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67 <param name="seq_fasta" type="data" format="fasta" label="Peptide Sequence Fasta"/>
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68 </when>
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69 <when value="tabular">
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70 <param name="seq_tsv" type="data" format="tabular" label="Peptide Sequence Tabular"/>
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71 <param name="pep_col" label="Select column with peptides" type="data_column" numerical="false" data_ref="seq_tsv" />
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72 <param name="id_col" label="Select column with name" type="data_column" numerical="false" data_ref="seq_tsv" optional="true"/>
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73 </when>
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74 <when value="entry">
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75 <param name="seq_text" type="text" size="80" label="Peptide Sequence"/>
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76 </when>
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77 </conditional>
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78 <conditional name="alleles">
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79 <param name="allelesrc" type="select" label="Alleles">
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80 <option value="history">From history</option>
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81 <option value="entry">Entered</option>
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82 </param>
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83 <when value="history">
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84 <param name="allele_file" type="data" format="txt" label="Alleles file"/>
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85 <help>The dataset should have on allele per line. The allele may be followed by an optional comma-separated list of pepttide lengths, e.g.: HLA-A*02:01,8,9</help>
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86 </when>
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87 <when value="entry">
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88 <param name="allele_text" type="text" size="80" label="Alleles">
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89 <help>Enter alleles separated by white space: HLA-A*03:01 HLA-B*07:02 (The peptide lengths may follow each allele: HLA-A*03:01,8,9,10 HLA-B*07:02,9</help>
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90 <validator type="regex" message="IDs separted by commas">^(HLA-([A-C]|D[PQR][AB]1)\*[0-9][[0-9]:[0-9][0-9](,(8|9|10|11|12|13|14|15))*)(\s+HLA-([A-C]|D[PQR][AB]1)\*[0-9][[0-9]:[0-9][0-9](,(8|9|10|11|12|13|14|15))*)*$</validator>
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91 </param>
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92 </when>
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93 </conditional>
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94 <param name="lengths" type="select" multiple="true" label="peptide lengths for prediction">
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95 <help>Used for any alleles which don't include specified lengths</help>
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96 <option value="8">8</option>
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97 <option value="9">9</option>
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98 <option value="10">10</option>
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99 <option value="11">11</option>
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100 <option value="12">12</option>
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101 <option value="13">13</option>
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102 <option value="14">14</option>
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103 <option value="15">15</option>
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104 </param>
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105 <conditional name="prediction">
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106 <param name="tool" type="select" label="Prediction">
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107 <option value="mhci">MHC-I Binding</option>
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108 <option value="mhcii">MHC-II Binding</option>
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109 <option value="processing">MHC-I Processing</option>
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110 <option value="mhcnp">MHC-NP T-Cell Epitope</option>
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111 <option value="bcell">Antibody Epitope Prediction</option>
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112 </param>
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113 <when value="mhci">
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114 <param name="method" type="select" label="prediction method">
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115 <option value="recommended" selected="true">recommended</option>
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116 <option value="consensus">consensus</option>
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117 <option value="netmhcpan">netmhcpan</option>
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118 <option value="ann">ann</option>
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119 <option value="smmpmbec">smmpmbec</option>
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120 <option value="smm">smm</option>
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121 <option value="comblib_sidney2008">comblib_sidney2008</option>
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122 <option value="netmhccons">netmhccons</option>
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123 <option value="pickpocket">pickpocket</option>
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124 </param>
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125 </when>
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126 <when value="mhcii">
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127 <param name="method" type="select" label="prediction method">
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128 <option value="recommended" selected="true">recommended</option>
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129 <option value="consensus3">consensus3</option>
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130 <option value="NetMHCIIpan">NetMHCIIpan</option>
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131 <option value="nn_align">nn_align</option>
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132 <option value="smm_align">smm_align</option>
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133 <option value="comblib">comblib</option>
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134 <option value="tepitope">tepitope</option>
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135 </param>
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136 </when>
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137 <when value="processing">
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138 <param name="method" type="select" label="prediction method">
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139 <option value="recommended" selected="true">recommended</option>
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140 <option value="consensus">consensus</option>
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141 <option value="netmhcpan">netmhcpan</option>
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142 <option value="ann">ann</option>
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143 <option value="smmpmbec">smmpmbec</option>
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144 <option value="smm">smm</option>
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145 <option value="comblib_sidney2008">comblib_sidney2008</option>
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146 </param>
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147 </when>
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148 <when value="mhcnp">
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149 <param name="method" type="select" label="prediction method">
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150 <option value="mhcnp" selected="true">mhcnp</option>
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151 </param>
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152 </when>
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153 <when value="bcell">
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154 <param name="method" type="select" label="prediction method">
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155 <option value="Bepipred" selected="true">Bepipred</option>
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156 <option value="Chou-Fasman">Chou-Fasman</option>
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157 <option value="Emini">Emini</option>
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158 <option value="Karplus-Schulz">Karplus-Schulz</option>
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159 <option value="Kolaskar-Tongaonkar">Kolaskar-Tongaonkar</option>
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160 <option value="Parker">Parker</option>
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161 </param>
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162 <param name="window_size" type="integer" value="" optional="true" min="1" label="window_size" help="window_size should be less than the sequence length, and less than 8 for Karplus-Schulz method"/>
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163 </when>
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164 </conditional>
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165 </inputs>
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166 <outputs>
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167 <data name="output" format="tabular"/>
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168 </outputs>
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169 <tests>
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170 <test>
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171 <param name="seqsrc" value="entry"/>
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172 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/>
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173 <param name="allelesrc" value="entry"/>
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174 <param name="allele_text" value="HLA-A*01:01,9"/>
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175 <param name="tool" value="mhci"/>
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176 <param name="method" value="recommended"/>
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177 <output name="output">
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178 <assert_contents>
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179 <has_text text="LYNTVATLY" />
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180 </assert_contents>
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181 </output>
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182 </test>
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183 <test>
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184 <param name="seqsrc" value="fasta"/>
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185 <param name="seq_fasta" ftype="fasta" value="seqs.fa"/>
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186 <param name="allelesrc" value="history"/>
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187 <param name="allele_file" ftype="txt" value="alleles.txt"/>
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188 <param name="tool" value="mhci"/>
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189 <param name="method" value="recommended"/>
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190 <output name="output">
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191 <assert_contents>
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192 <has_text text="peptide1" />
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193 <has_text text="AHKVPRRLLK" />
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194 </assert_contents>
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195 </output>
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196 </test>
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197 <test>
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198 <param name="seqsrc" value="tabular"/>
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199 <param name="seq_tsv" ftype="tabular" value="seqs.tsv"/>
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200 <param name="pep_col" value="3"/>
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201 <param name="id_col" value="1"/>
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202 <param name="allelesrc" value="history"/>
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203 <param name="allele_file" ftype="txt" value="alleles.txt"/>
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204 <param name="tool" value="mhci"/>
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205 <param name="method" value="recommended"/>
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206 <output name="output">
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207 <assert_contents>
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208 <has_text text="peptide1" />
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209 <has_text text="AHKVPRRLLK" />
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210 </assert_contents>
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211 </output>
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212 </test>
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213 </tests>
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214 <help><![CDATA[
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215 The IEDB is a free resource, funded by a contract from the National Institute of Allergy and Infectious Diseases. It offers easy searching of experimental data characterizing antibody and T cell epitopes studied in humans, non-human primates, and other animal species.
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216
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217 This tool retrieves epitope information about input peptide sequences by using the RESTful web services provided by IEDB.
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218 The webservices are described at: http://tools.immuneepitope.org/main/tools-api/
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219
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220 **INPUTS**
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221
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222 peptide sequences from a fasta file or a column in a tabular file
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223
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224 HLA alleles either entered as text or on per line in a text file
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225
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226
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227 **OUTPUTS**
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228
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229 A tabular file containing the results returned from the IEDB web service
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230
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231 ]]></help>
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232 <citations>
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233 <citation type="doi">10.1093/nar/gku938</citation>
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234 </citations>
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235 </tool>
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