Mercurial > repos > jjohnson > iedb_api

annotate iedb_api.xml @ 2:883cdf0ffae5 draft

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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
author jjohnson
date Wed, 26 Feb 2020 15:02:37 -0500
parents 4a89ba6cfc63
children 153d5fa7af53
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4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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1 <tool id="iedb_api" name="IEDB" version="2.15.0">
0
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2 <description>MHC Binding prediction</description>
1
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3 <macros>
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4 <xml name="alleles" token_hla_regex="" token_hla_examples="" token_hlalen_examples="">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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5 <conditional name="alleles">
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6 <param name="allelesrc" type="select" label="Alleles">
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7 <option value="history">From history</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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8 <option value="entry">Entered</option>
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9 </param>
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10 <when value="history">
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11 <param name="allele_file" type="data" format="txt" label="Alleles file">
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12 <help>The dataset should have on allele per line. The allele may be followed by an optional comma-separated list of peptide lengths, e.g.: @HLALEN_EXAMPLES@</help>
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13 </param>
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14 </when>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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15 <when value="entry">
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16 <param name="allele_text" type="text" size="80" label="Alleles">
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17 <help>Enter alleles separated by white space: @HLA_EXAMPLES@ (The peptide lengths may follow each allele: @HLALEN_EXAMPLES@)</help>
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18 <validator type="regex" message="Doesn't appear to be a valid allele">^@HLA_REGEX@(\s+@HLA_REGEX@)*$</validator>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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19 </param>
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20 </when>
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21 </conditional>
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22 </xml>
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23 </macros>
0
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24 <requirements>
1
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25 <requirement type="package" version="3.7">python</requirement>
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26 </requirements>
1
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27 <command detect_errors="exit_code"><![CDATA[
0
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28 #import re
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29 python '${__tool_directory__}/iedb_api.py'
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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30 --prediction=$prediction.tool
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31 --method=$prediction.method
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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32 #if $prediction.tool == 'bcell':
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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33 #if $prediction.window_size:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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34 -w $prediction.window_size
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35 #end if
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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36 #else
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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37 #if $prediction.tool == 'processing' and $prediction.proteasome:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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38 --proteasome $prediction.proteasome
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39 #end if
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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40 #if $prediction.alleles.allelesrc == 'history':
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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41 #for $line in open(str($prediction.alleles.allele_file)):
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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42 #set $fields = $line.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 $alen in str($prediction.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 #else:
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57 #for $word in str($prediction.alleles.allele_text).strip().split():
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58 #set $fields = $word.strip().split(',')
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59 #set $allele = $fields[0].strip()
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60 #if len($allele) > 0:
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61 #if len($fields) > 1:
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62 #for $alen in $fields[1:]:
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63 -a '$allele' -l $alen
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64 #end for
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65 #else:
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66 #for $alen in str($prediction.lengths).split(','):
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67 -a '$allele' -l $alen
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68 #end for
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69 #end if
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70 #end if
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71 #end for
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72 #end if
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73 #end if
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74
0
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75 #if $sequence.seqsrc == 'fasta':
1
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76 -i '$sequence.seq_fasta'
0
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77 #else if $sequence.seqsrc == 'tabular':
1
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78 -i '$sequence.seq_tsv'
0
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79 -c #echo int(str($sequence.pep_col)) - 1
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80 #if $sequence.id_col:
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81 -C #echo int(str($sequence.id_col)) - 1
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82 #end if
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83 #else:
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84 #for $seq in str($sequence.seq_text).strip().split():
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85 -s $seq.strip()
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86 #end for
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87 #end if
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88 -o $output
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89 ]]></command>
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90 <inputs>
1
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91 <conditional name="prediction">
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92 <param name="tool" type="select" label="Prediction">
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93 <option value="mhci">MHC-I Binding</option>
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94 <option value="mhcii">MHC-II Binding</option>
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95 <option value="processing">MHC-I Processing</option>
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96 <option value="mhcnp">MHC-NP T-Cell Epitope</option>
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97 <option value="bcell">Antibody Epitope Prediction</option>
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98 </param>
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99 <when value="mhci">
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100 <param name="method" type="select" label="prediction method">
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101 <option value="recommended" selected="true">recommended</option>
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102 <option value="consensus">consensus</option>
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103 <option value="netmhcpan">netmhcpan</option>
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104 <option value="ann">ann</option>
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105 <option value="smmpmbec">smmpmbec</option>
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106 <option value="smm">smm</option>
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107 <option value="comblib_sidney2008">comblib_sidney2008</option>
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108 <option value="netmhccons">netmhccons</option>
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109 <option value="pickpocket">pickpocket</option>
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110 </param>
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111 <expand macro="alleles" hla_regex="(HLA-[A-CEG]\*[0-8][[0-9]:[0-9][0-9][0-9]*|BoLA-.+|Gogo-.+|H-2-[DKL][bdk]|Mamu-.+|Patr-.+|RT.+|SLA-.+)(,([8-9]|1[0-5]))*" hla_examples="HLA-A*03:01 HLA-B*07:02" hlalen_examples="HLA-A*03:01,8,9,10 HLA-B*07:02,9"/>
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112 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
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113 <help>Used for any alleles which don't include specified lengths</help>
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114 <option value="8" selected="true">8</option>
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115 <option value="9">9</option>
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116 <option value="10">10</option>
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117 <option value="11">11</option>
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118 <option value="12">12</option>
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119 <option value="13">13</option>
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120 <option value="14">14</option>
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121 <option value="15">15</option>
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122 </param>
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123
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124 </when>
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125 <when value="mhcii">
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126 <param name="method" type="select" label="prediction method">
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127 <option value="recommended" selected="true">recommended</option>
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128 <option value="consensus3">consensus3</option>
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129 <option value="NetMHCIIpan">NetMHCIIpan</option>
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130 <option value="nn_align">nn_align</option>
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131 <option value="smm_align">smm_align</option>
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132 <option value="comblib">comblib</option>
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133 <option value="tepitope">tepitope</option>
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134 </param>
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135 <expand macro="alleles" hla_regex="((DPA1\*0[1-3](:0[1-3])?/DPB1\*0[1-6]:0[12]|DQA1\*0[1-5]:0[12]/DQB1\*0[2-6]:0[12]|DRB[1-5]\*[01][1-9]:0[1-5]|H2-IA[bd]),(asis|[1-2][0-9]|30))*" hla_examples="DPA1*01/DPB1*04:01 HLA-DRB1*01:01 H2-IAb" hlalen_examples="DPA1*01/DPB1*04:01,11,15"/>
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136 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
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137 <help>Used for any alleles which don't include specified lengths</help>
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138 <option value="asis">asis</option>
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139 <option value="11">11</option>
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140 <option value="12">12</option>
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141 <option value="13">13</option>
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142 <option value="14">14</option>
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143 <option value="15" selected="true">15</option>
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144 <option value="16">16</option>
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145 <option value="17">17</option>
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146 <option value="18">18</option>
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147 <option value="19">19</option>
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148 <option value="20">20</option>
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149 <option value="21">21</option>
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150 <option value="22">22</option>
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151 <option value="23">23</option>
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152 <option value="24">24</option>
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153 <option value="25">25</option>
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154 <option value="26">26</option>
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155 <option value="27">27</option>
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156 <option value="28">28</option>
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157 <option value="29">29</option>
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158 <option value="30">30</option>
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159 </param>
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160 </when>
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161 <when value="processing">
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162 <param name="method" type="select" label="prediction method">
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163 <option value="recommended" selected="true">recommended</option>
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164 <option value="consensus">consensus</option>
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165 <option value="netmhcpan">netmhcpan</option>
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166 <option value="ann">ann</option>
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167 <option value="smmpmbec">smmpmbec</option>
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168 <option value="smm">smm</option>
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169 <option value="comblib_sidney2008">comblib_sidney2008</option>
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170 </param>
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171 <param name="proteasome" type="select" label="proteasome type">
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172 <option value="immuno">immuno</option>
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173 <option value="constitutive">constitutive</option>
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174 </param>
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175 <expand macro="alleles" hla_regex="(HLA-[A-CE]\*[0-8][[0-9]:[0-9][0-9]|BoLA-.+|Gogo-.+|H-2-[DKL][bdk]|Mamu-.+|Patr-.+|RT.+|SLA-.+)(,([8-9]|1[0-4]))*" hla_examples="HLA-A*03:01 HLA-B*07:02" hlalen_examples="HLA-A*03:01,8,9,10 HLA-B*07:02,9"/>
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176 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
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177 <help>Used for any alleles which don't include specified lengths</help>
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178 <option value="8" selected="true">8</option>
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179 <option value="9">9</option>
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180 <option value="10">10</option>
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181 <option value="11">11</option>
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182 <option value="12">12</option>
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183 <option value="13">13</option>
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184 <option value="14">14</option>
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185 </param>
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186 </when>
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187 <when value="mhcnp">
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188 <param name="method" type="select" label="prediction method">
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189 <option value="mhcnp" selected="true">mhcnp</option>
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190 <option value="netmhcpan">netmhcpan</option>
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191 </param>
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192 <expand macro="alleles" hla_regex="(HLA-(A\*02:01|B\*07:02|B\*35:01|B\*44:03|B\*53:01|B\*57:01)|H-2-[DK]b)(,[8-9]|1[0-1])*" hla_examples="HLA-A*02:01 H-2-Db" hlalen_examples="HLA-A*02:01,8,9,10"/>
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193 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
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194 <help>Used for any alleles which don't include specified lengths</help>
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195 <option value="8" selected="true">8</option>
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196 <option value="9">9</option>
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197 <option value="10">10</option>
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198 <option value="11">11</option>
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199 </param>
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200 </when>
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201 <when value="bcell">
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202 <param name="method" type="select" label="prediction method">
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203 <option value="Bepipred" selected="true">Bepipred</option>
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204 <option value="Chou-Fasman">Chou-Fasman</option>
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205 <option value="Emini">Emini</option>
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206 <option value="Karplus-Schulz">Karplus-Schulz</option>
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207 <option value="Kolaskar-Tongaonkar">Kolaskar-Tongaonkar</option>
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208 <option value="Parker">Parker</option>
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209 </param>
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210 <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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211 </when>
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212 </conditional>
0
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213 <conditional name="sequence">
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214 <param name="seqsrc" type="select" label="Peptide sequences">
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215 <option value="fasta">Fasta file</option>
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216 <option value="tabular">From tabular</option>
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217 <option value="entry"></option>
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218 </param>
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219 <when value="fasta">
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220 <param name="seq_fasta" type="data" format="fasta" label="Peptide Sequence Fasta"/>
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221 </when>
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222 <when value="tabular">
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223 <param name="seq_tsv" type="data" format="tabular" label="Peptide Sequence Tabular"/>
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224 <param name="pep_col" label="Select column with peptides" type="data_column" numerical="false" data_ref="seq_tsv" />
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225 <param name="id_col" label="Select column with name" type="data_column" numerical="false" data_ref="seq_tsv" optional="true"/>
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226 </when>
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227 <when value="entry">
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228 <param name="seq_text" type="text" size="80" label="Peptide Sequence"/>
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229 </when>
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230 </conditional>
1
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231
0
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232 </inputs>
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233 <outputs>
1
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234 <!--
0
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235 <data name="output" format="tabular"/>
1
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236 -->
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237 <data name="output" format="tabular" label="IEDB ${prediction.tool} ${prediction.method}"/>
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238 <data name="output2" format="tabular" label="IEDB ${prediction.tool} ${prediction.method} residue scores" from_work_dir="iedb_results2">
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239 <filter>prediction['method'].startswith('Bepipred')</filter>
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240 </data>
0
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241 </outputs>
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242 <tests>
1
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243 <!-- test1 -->
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244 <test>
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245 <conditional name="prediction">
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246 <param name="tool" value="mhci"/>
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247 <param name="method" value="recommended"/>
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248 <conditional name="alleles">
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249 <param name="allelesrc" value="entry"/>
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250 <param name="allele_text" value="HLA-A*01:01,9"/>
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251 </conditional>
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252 </conditional>
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253 <conditional name="sequence">
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254 <param name="seqsrc" value="entry"/>
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255 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/>
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256 </conditional>
0
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257 <output name="output">
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258 <assert_contents>
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259 <has_text text="LYNTVATLY" />
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diff changeset
260 </assert_contents>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
261 </output>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
262 </test>
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
263 <!-- test2 -->
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
264 <test>
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
265 <conditional name="prediction">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
266 <param name="tool" value="mhci"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
267 <param name="method" value="recommended"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
268 <conditional name="alleles">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
269 <param name="allelesrc" value="history"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
270 <param name="allele_file" ftype="tabular" value="alleles.tsv"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
271 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
272 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
273 <conditional name="sequence">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
274 <param name="seqsrc" value="fasta"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
275 <param name="seq_fasta" ftype="fasta" value="seqs.fa"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
276 </conditional>
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
277 <output name="output">
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
278 <assert_contents>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
279 <has_text text="peptide1" />
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
280 <has_text text="HKVPRRLLK" />
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
281 </assert_contents>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
282 </output>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
283 </test>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
284 <!-- test3 -->
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
285 <test>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
286 <conditional name="prediction">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
287 <param name="tool" value="mhci"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
288 <param name="method" value="recommended"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
289 <conditional name="alleles">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
290 <param name="allelesrc" value="history"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
291 <param name="allele_file" ftype="tabular" value="alleles.tsv"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
292 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
293 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
294 <conditional name="sequence">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
295 <param name="seqsrc" value="tabular"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
296 <param name="seq_tsv" ftype="tabular" value="seqs.tsv"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
297 <param name="pep_col" value="3"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
298 <param name="id_col" value="1"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
299 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
300 <output name="output">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
301 <assert_contents>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
302 <has_text text="peptide1" />
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
303 <has_text text="HKVPRRLLK" />
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
304 </assert_contents>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
305 </output>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
306 </test>
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
307 <!-- test4 -->
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
308 <test>
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
309 <conditional name="prediction">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
310 <param name="tool" value="mhcii"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
311 <param name="method" value="recommended"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
312 <conditional name="alleles">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
313 <param name="allelesrc" value="entry"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
314 <param name="allele_text" value="DPA1*01/DPB1*04:01"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
315 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
316 <param name="lengths" value="asis"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
317 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
318 <conditional name="sequence">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
319 <param name="seqsrc" value="entry"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
320 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
321 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
322 <output name="output">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
323 <assert_contents>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
324 <has_text text="LYNTVATLY" />
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
325 </assert_contents>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
326 </output>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
327 </test>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
328 <!-- test5 -->
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
329 <test>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
330 <conditional name="prediction">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
331 <param name="tool" value="processing"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
332 <param name="method" value="recommended"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
333 <conditional name="alleles">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
334 <param name="allelesrc" value="entry"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
335 <param name="allele_text" value="HLA-A*01:01,8 HLA-A*02:01,9"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
336 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
337 <param name="proteasome" value="constitutive"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
338 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
339 <conditional name="sequence">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
340 <param name="seqsrc" value="entry"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
341 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
342 </conditional>
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
343 <output name="output">
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
344 <assert_contents>
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
345 <has_text text="LYNTVATLY" />
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
346 </assert_contents>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
347 </output>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
348 </test>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
349 <!-- test6 -->
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
350 <test>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
351 <conditional name="prediction">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
352 <param name="tool" value="mhcnp"/>
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353 <param name="method" value="mhcnp"/>
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354 <conditional name="alleles">
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355 <param name="allelesrc" value="entry"/>
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356 <param name="allele_text" value="HLA-A*02:01,9"/>
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357 </conditional>
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358 </conditional>
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359 <conditional name="sequence">
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360 <param name="seqsrc" value="entry"/>
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361 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/>
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362 </conditional>
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363 <output name="output">
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364 <assert_contents>
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365 <has_text text="LYNTVATLY" />
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366 </assert_contents>
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367 </output>
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368 </test>
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369 <!-- test7 -->
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370 <test>
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371 <conditional name="prediction">
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372 <param name="tool" value="bcell"/>
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373 <param name="method" value="Emini"/>
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374 </conditional>
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375 <conditional name="sequence">
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376 <param name="seqsrc" value="entry"/>
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377 <param name="seq_text" value="VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTE"/>
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378 </conditional>
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379 <output name="output">
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380 <assert_contents>
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381 <has_text text="VLSEGE" />
0
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382 </assert_contents>
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383 </output>
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384 </test>
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385 </tests>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
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386 <help><![CDATA[
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
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387 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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388
1
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389 This tool retrieves epitope binding information about input peptide sequences by using the RESTful web services provided by IEDB.
0
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390 The webservices are described at: http://tools.immuneepitope.org/main/tools-api/
1
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391 That page also describes how to retrieve the available HLA alleles for class of epitope binding.
0
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392
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393 **INPUTS**
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394
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395 peptide sequences from a fasta file or a column in a tabular file
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396
1
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397 HLA alleles either entered as text or one per line in a text file
0
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398
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399
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
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400 **OUTPUTS**
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401
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402 A tabular file containing the results returned from the IEDB web service
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403
2
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404 **Typical Workflow for Human MHC I Binding Prediction**
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405
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
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406 The RNAseq data for the subject would be used for:
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407
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
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408 - HLA prediction by seq2HLA_
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409 - Novel Antigen Prediction by a variety of workflows to generate a Antigen peptide fasta
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410
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411 .. _seq2HLA: https://toolshed.g2.bx.psu.edu/view/iuc/seq2hla/52bba1cd3823
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412
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
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413 .. image:: $PATH_TO_IMAGES/IEDB_Workflow_QueryTabular.png
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414 :width: 584
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415 :height: 430
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416
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
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417 .. note:: The seq2HLA ClassI.HLAgenotype4digits output needs to be converted for IEDB alleles.
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418
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419 The seq2HLA ClassI.HLAgenotype4digits output:
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420
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421 .. image:: $PATH_TO_IMAGES/seq2HLA_ClassI.HLAgenotype4digits.png
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422 :width: 285
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423 :height: 77
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424
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
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425 Needs to be converted into IEDB formatted alleles:
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426
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
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427 .. image:: $PATH_TO_IMAGES/IEDB_formatted_alleles.png
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428 :width: 74
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429 :height: 81
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430
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431 In the workflow above QueryTabular_ tool converts the alleles:
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432
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433 - Filter Dataset Input
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434
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435 * skip leading lines - *skip lines:* 1
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436 * select columns - *columns:* 2,4
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437 * regex replace value in column - *column:* 1 *regex pattern:* ^(\\w+[*]\\d\\d:\\d\\d\\d?).*$ *replacement expression:* HLA-\\1
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438 * regex replace value in column - *column:* 2 *regex pattern:* ^(\\w+[*]\\d\\d:\\d\\d\\d?).*$ *replacement expression:* HLA-\\1
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439
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
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440 - SQL Query to generate tabular output
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441
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442 * SELECT c1 FROM t1 UNION SELECT c2 FROM t1
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443
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
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diff changeset
444 .. _QueryTabular: https://toolshed.g2.bx.psu.edu/view/iuc/query_tabular/0c95a3f1654f
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
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diff changeset
445
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
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446
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
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diff changeset
447 The IEDB formatting can also be performed by TextProcessing_ tools:
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
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448
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
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449 .. _TextProcessing: https://toolshed.g2.bx.psu.edu/view/bgruening/text_processing/0a8c6b61f0f4
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
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450
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
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451 .. image:: $PATH_TO_IMAGES/TextProcessingConversion.png
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
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452 :width: 608
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
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453 :height: 87
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
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454
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
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455 The TextProcessing steps to convert the alleles:
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
456
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
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457 - Remove beginning - removes the header line
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
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458 - Replace Text - picks Allele 1 and Allele 2 from each line and reformats each on a separate line
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
459
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
460 * *Find pattern:* ^.*\\t([a-zA-Z]+[*][0-9]{2}:[0-9]{2,3}).*\\t.*\\t([a-zA-Z]+[*][0-9]{2}:[0-9]{2,3}).*\\t.*$
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
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461 * *Replace with:* HLA-\\1\\nHLA-\\2
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
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462
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
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463 - Unique - remove duplicates
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
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464
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
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465
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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466 ]]></help>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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467 <citations>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
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468 <citation type="doi">10.1093/nar/gku938</citation>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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469 </citations>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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470 </tool>