Mercurial > repos > iuc > iedb_api

annotate iedb_api.xml @ 0:fe3c43451319 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
author iuc
date Fri, 28 Feb 2020 18:09:34 -0500
parents
children a09849898387
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fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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1 <tool id="iedb_api" name="IEDB" version="2.15.0">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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2 <description>MHC Binding prediction</description>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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3 <macros>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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4 <xml name="alleles" token_hla_regex="" token_hla_examples="" token_hlalen_examples="">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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5 <conditional name="alleles">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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6 <param name="allelesrc" type="select" label="Alleles">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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7 <option value="history">From history</option>
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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">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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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>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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13 </param>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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14 </when>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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15 <when value="entry">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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16 <param name="allele_text" type="text" size="80" label="Alleles">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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17 <help>Enter alleles separated by white space: @HLA_EXAMPLES@ (The peptide lengths may follow each allele: @HLALEN_EXAMPLES@)</help>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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18 <validator type="regex" message="Doesn't appear to be a valid allele">^@HLA_REGEX@(\s+@HLA_REGEX@)*$</validator>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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19 </param>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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20 </when>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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21 </conditional>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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22 </xml>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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23 </macros>
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24 <requirements>
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25 <requirement type="package" version="3.7">python</requirement>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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26 </requirements>
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27
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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28 <command detect_errors="exit_code"><![CDATA[
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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29 #import re
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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30 python '${__tool_directory__}/iedb_api.py'
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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31 --prediction=$prediction.tool
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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32 --method=$prediction.method
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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33 #if $prediction.tool == 'bcell':
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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34 #if $prediction.window_size:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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35 -w $prediction.window_size
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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36 #end if
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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37 #else
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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38 #if $prediction.tool == 'processing' and $prediction.proteasome:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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39 --proteasome $prediction.proteasome
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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40 #end if
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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41 #if $prediction.alleles.allelesrc == 'history':
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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42 -A '$prediction.alleles.allele_file'
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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43 #else:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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44 -A '$entered_alleles'
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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45 #end if
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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46 #end if
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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47
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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48 #if $sequence.seqsrc == 'fasta':
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49 -i '$sequence.seq_fasta'
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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50 #else if $sequence.seqsrc == 'tabular':
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51 -i '$sequence.seq_tsv'
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52 -c #echo int(str($sequence.pep_col)) - 1
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53 #if $sequence.id_col:
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54 -C #echo int(str($sequence.id_col)) - 1
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55 #end if
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56 #else:
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57 -i '$entered_seqs' -c 1 -C 0
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58 #end if
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59 -o '$output'
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60 ]]></command>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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61 <configfiles>
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62 <configfile name="entered_alleles"><![CDATA[#slurp
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63 #if $prediction.tool != 'bcell' and $prediction.alleles.allelesrc == 'entry'
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64 #for $word in str($prediction.alleles.allele_text).strip().split():
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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65 #if $word.find(',') > 0
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66 $word
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67 #else
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68 #set $allele = $word + ',' + str($prediction.lengths)
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69 $allele
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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 ]]></configfile>
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74 <configfile name="entered_seqs"><![CDATA[#slurp
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75 #if $sequence.seqsrc == 'entry'
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76 #for $i, $seq in enumerate(str($sequence.seq_text).strip().split())
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77 #set $seqid = $i + 1
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78 #set $seqtext = '\t'.join([str($seqid),$seq.strip()])
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79 $seqtext
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80 #end for
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81 #end if
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82 ]]></configfile>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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83 </configfiles>
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84 <inputs>
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85 <conditional name="prediction">
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86 <param name="tool" type="select" label="Prediction">
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87 <option value="mhci">MHC-I Binding</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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88 <option value="mhcii">MHC-II Binding</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
89 <option value="processing">MHC-I Processing</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
90 <option value="mhcnp">MHC-NP T-Cell Epitope</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
91 <option value="bcell">Antibody Epitope Prediction</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
92 </param>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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93 <when value="mhci">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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94 <param name="method" type="select" label="prediction method">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
95 <option value="recommended" selected="true">recommended</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
96 <option value="consensus">consensus</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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97 <option value="netmhcpan">netmhcpan</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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98 <option value="ann">ann</option>
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iuc
parents:
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99 <option value="smmpmbec">smmpmbec</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
100 <option value="smm">smm</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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101 <option value="comblib_sidney2008">comblib_sidney2008</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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102 <option value="netmhccons">netmhccons</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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103 <option value="pickpocket">pickpocket</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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104 </param>
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iuc
parents:
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105 <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"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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diff changeset
106 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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107 <help>Used for any alleles which don't include specified lengths</help>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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108 <option value="8" selected="true">8</option>
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iuc
parents:
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109 <option value="9">9</option>
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iuc
parents:
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110 <option value="10">10</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
111 <option value="11">11</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
112 <option value="12">12</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
113 <option value="13">13</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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114 <option value="14">14</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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115 <option value="15">15</option>
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iuc
parents:
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116 </param>
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iuc
parents:
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117
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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118 </when>
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iuc
parents:
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119 <when value="mhcii">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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120 <param name="method" type="select" label="prediction method">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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121 <option value="recommended" selected="true">recommended</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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122 <option value="consensus3">consensus3</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
123 <option value="NetMHCIIpan">NetMHCIIpan</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
124 <option value="nn_align">nn_align</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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125 <option value="smm_align">smm_align</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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126 <option value="comblib">comblib</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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127 <option value="tepitope">tepitope</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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128 </param>
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iuc
parents:
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129 <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]|(HLA-)?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"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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130 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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131 <help>Used for any alleles which don't include specified lengths</help>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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132 <option value="asis">asis</option>
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iuc
parents:
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133 <option value="11">11</option>
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iuc
parents:
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134 <option value="12">12</option>
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iuc
parents:
diff changeset
135 <option value="13">13</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
136 <option value="14">14</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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137 <option value="15" selected="true">15</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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138 <option value="16">16</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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139 <option value="17">17</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
140 <option value="18">18</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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141 <option value="19">19</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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142 <option value="20">20</option>
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iuc
parents:
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143 <option value="21">21</option>
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iuc
parents:
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144 <option value="22">22</option>
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iuc
parents:
diff changeset
145 <option value="23">23</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
146 <option value="24">24</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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147 <option value="25">25</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
148 <option value="26">26</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
149 <option value="27">27</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
150 <option value="28">28</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
151 <option value="29">29</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
152 <option value="30">30</option>
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iuc
parents:
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153 </param>
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iuc
parents:
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154 </when>
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iuc
parents:
diff changeset
155 <when value="processing">
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iuc
parents:
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156 <param name="method" type="select" label="prediction method">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
157 <option value="recommended" selected="true">recommended</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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158 <option value="consensus">consensus</option>
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iuc
parents:
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159 <option value="netmhcpan">netmhcpan</option>
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iuc
parents:
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160 <option value="ann">ann</option>
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iuc
parents:
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161 <option value="smmpmbec">smmpmbec</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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162 <option value="smm">smm</option>
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iuc
parents:
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163 <option value="comblib_sidney2008">comblib_sidney2008</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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164 </param>
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iuc
parents:
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165 <param name="proteasome" type="select" label="proteasome type">
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iuc
parents:
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166 <option value="immuno">immuno</option>
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iuc
parents:
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167 <option value="constitutive">constitutive</option>
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iuc
parents:
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168 </param>
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iuc
parents:
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169 <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"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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170 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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171 <help>Used for any alleles which don't include specified lengths</help>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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172 <option value="8" selected="true">8</option>
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173 <option value="9">9</option>
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iuc
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174 <option value="10">10</option>
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iuc
parents:
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175 <option value="11">11</option>
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iuc
parents:
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176 <option value="12">12</option>
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iuc
parents:
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177 <option value="13">13</option>
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iuc
parents:
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178 <option value="14">14</option>
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179 </param>
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180 </when>
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iuc
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181 <when value="mhcnp">
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iuc
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182 <param name="method" type="select" label="prediction method">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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183 <option value="mhcnp" selected="true">mhcnp</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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184 <option value="netmhcpan">netmhcpan</option>
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185 </param>
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iuc
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186 <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"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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187 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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188 <help>Used for any alleles which don't include specified lengths</help>
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iuc
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189 <option value="8" selected="true">8</option>
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iuc
parents:
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190 <option value="9">9</option>
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iuc
parents:
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191 <option value="10">10</option>
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iuc
parents:
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192 <option value="11">11</option>
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193 </param>
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194 </when>
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iuc
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195 <when value="bcell">
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iuc
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196 <param name="method" type="select" label="prediction method">
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iuc
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197 <option value="Bepipred" selected="true">Bepipred</option>
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198 <option value="Chou-Fasman">Chou-Fasman</option>
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iuc
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199 <option value="Emini">Emini</option>
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iuc
parents:
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200 <option value="Karplus-Schulz">Karplus-Schulz</option>
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iuc
parents:
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201 <option value="Kolaskar-Tongaonkar">Kolaskar-Tongaonkar</option>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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202 <option value="Parker">Parker</option>
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203 </param>
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iuc
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204 <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"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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205 </when>
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206 </conditional>
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iuc
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207 <conditional name="sequence">
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208 <param name="seqsrc" type="select" label="Peptide sequences">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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209 <option value="fasta">Fasta file</option>
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iuc
parents:
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210 <option value="tabular">From tabular</option>
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iuc
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211 <option value="entry"></option>
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212 </param>
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iuc
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213 <when value="fasta">
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214 <param name="seq_fasta" type="data" format="fasta" label="Peptide Sequence Fasta"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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215 </when>
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216 <when value="tabular">
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iuc
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217 <param name="seq_tsv" type="data" format="tabular" label="Peptide Sequence Tabular"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
218 <param name="pep_col" label="Select column with peptides" type="data_column" numerical="false" data_ref="seq_tsv" />
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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219 <param name="id_col" label="Select column with name" type="data_column" numerical="false" data_ref="seq_tsv" optional="true"/>
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220 </when>
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iuc
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221 <when value="entry">
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222 <param name="seq_text" type="text" label="Peptide Sequence"/>
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223 </when>
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224 </conditional>
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225
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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226 </inputs>
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227 <outputs>
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228 <!--
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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229 <data name="output" format="tabular"/>
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iuc
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230 -->
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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231 <data name="output" format="tabular" label="IEDB ${prediction.tool} ${prediction.method}"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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232 <data name="output2" format="tabular" label="IEDB ${prediction.tool} ${prediction.method} residue scores" from_work_dir="iedb_results2">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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233 <filter>prediction['method'].startswith('Bepipred')</filter>
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234 </data>
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235 </outputs>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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236 <tests>
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237 <!-- test1 -->
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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238 <test>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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239 <conditional name="prediction">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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240 <param name="tool" value="mhci"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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241 <param name="method" value="recommended"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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242 <conditional name="alleles">
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iuc
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243 <param name="allelesrc" value="entry"/>
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iuc
parents:
diff changeset
244 <param name="allele_text" value="HLA-A*01:01,9"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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245 </conditional>
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246 </conditional>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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parents:
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247 <conditional name="sequence">
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iuc
parents:
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248 <param name="seqsrc" value="entry"/>
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iuc
parents:
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249 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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250 </conditional>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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251 <output name="output">
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iuc
parents:
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252 <assert_contents>
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iuc
parents:
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253 <has_text text="LYNTVATLY" />
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254 </assert_contents>
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255 </output>
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256 </test>
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parents:
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257 <!-- test2 -->
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258 <test>
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iuc
parents:
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259 <conditional name="prediction">
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iuc
parents:
diff changeset
260 <param name="tool" value="mhci"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
261 <param name="method" value="recommended"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
262 <conditional name="alleles">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
263 <param name="allelesrc" value="history"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
264 <param name="allele_file" ftype="tabular" value="alleles.tsv"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
265 </conditional>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
266 </conditional>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
267 <conditional name="sequence">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
268 <param name="seqsrc" value="fasta"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
269 <param name="seq_fasta" ftype="fasta" value="seqs.fa"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
270 </conditional>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
271 <output name="output">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
272 <assert_contents>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
273 <has_text text="peptide1" />
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
274 <has_text text="HKVPRRLLK" />
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
275 </assert_contents>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
276 </output>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
277 </test>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
278 <!-- test3 -->
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
279 <test>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
280 <conditional name="prediction">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
281 <param name="tool" value="mhci"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
282 <param name="method" value="recommended"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
283 <conditional name="alleles">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
284 <param name="allelesrc" value="history"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
285 <param name="allele_file" ftype="tabular" value="alleles.tsv"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
286 </conditional>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
287 </conditional>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
288 <conditional name="sequence">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
289 <param name="seqsrc" value="tabular"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
290 <param name="seq_tsv" ftype="tabular" value="seqs.tsv"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
291 <param name="pep_col" value="3"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
292 <param name="id_col" value="1"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
293 </conditional>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
294 <output name="output">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
295 <assert_contents>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
296 <has_text text="peptide1" />
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
297 <has_text text="HKVPRRLLK" />
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
298 </assert_contents>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
299 </output>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
300 </test>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
301 <!-- test4 -->
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
302 <test>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
303 <conditional name="prediction">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
304 <param name="tool" value="mhcii"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
305 <param name="method" value="recommended"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
306 <conditional name="alleles">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
307 <param name="allelesrc" value="entry"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
308 <param name="allele_text" value="DPA1*01/DPB1*04:01"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
309 </conditional>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
310 <param name="lengths" value="asis"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
311 </conditional>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
312 <conditional name="sequence">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
313 <param name="seqsrc" value="entry"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
314 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
315 </conditional>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
316 <output name="output">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
317 <assert_contents>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
318 <has_text text="LYNTVATLY" />
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
319 </assert_contents>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
320 </output>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
321 </test>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
322 <!-- test5 -->
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
323 <test>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
324 <conditional name="prediction">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
325 <param name="tool" value="processing"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
326 <param name="method" value="recommended"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
327 <conditional name="alleles">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
328 <param name="allelesrc" value="entry"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
329 <param name="allele_text" value="HLA-A*01:01,8 HLA-A*02:01,9"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
330 </conditional>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
331 <param name="proteasome" value="constitutive"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
332 </conditional>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
333 <conditional name="sequence">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
334 <param name="seqsrc" value="entry"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
335 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
336 </conditional>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
337 <output name="output">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
338 <assert_contents>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
339 <has_text text="LYNTVATLY" />
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
340 </assert_contents>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
341 </output>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
342 </test>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
343 <!-- test6 -->
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
344 <test>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
345 <conditional name="prediction">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
346 <param name="tool" value="mhcnp"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
347 <param name="method" value="mhcnp"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
348 <conditional name="alleles">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
349 <param name="allelesrc" value="entry"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
350 <param name="allele_text" value="HLA-A*02:01,9"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
351 </conditional>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
352 </conditional>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
353 <conditional name="sequence">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
354 <param name="seqsrc" value="entry"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
355 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
356 </conditional>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
357 <output name="output">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
358 <assert_contents>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
359 <has_text text="LYNTVATLY" />
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
360 </assert_contents>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
361 </output>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
362 </test>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
363 <!-- test7 -->
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
364 <test>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
365 <conditional name="prediction">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
366 <param name="tool" value="bcell"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
367 <param name="method" value="Emini"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
368 </conditional>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
369 <conditional name="sequence">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
370 <param name="seqsrc" value="entry"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
371 <param name="seq_text" value="VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTE"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
372 </conditional>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
373 <output name="output">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
374 <assert_contents>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
375 <has_text text="VLSEGE" />
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
376 </assert_contents>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
377 </output>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
378 </test>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
379 <!-- test8 -->
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
380 <test>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
381 <conditional name="prediction">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
382 <param name="tool" value="bcell"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
383 <param name="method" value="Bepipred"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
384 <param name="window_size" value="9"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
385 </conditional>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
386 <conditional name="sequence">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
387 <param name="seqsrc" value="fasta"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
388 <param name="seq_fasta" ftype="fasta" value="bcell.fa"/>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
389 </conditional>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
390 <output name="output">
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
391 <assert_contents>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
392 <has_text text="ADVAGH" />
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
393 </assert_contents>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
394 </output>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
395 </test>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
396
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
397 </tests>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
398 <help><![CDATA[
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
399 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.
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
400
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
401 This tool retrieves epitope binding information about input peptide sequences by using the RESTful web services provided by IEDB.
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
402 The webservices are described at: http://tools.immuneepitope.org/main/tools-api/
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
403 That page also describes how to retrieve the available HLA alleles for class of epitope binding.
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
404
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
405 **INPUTS**
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
406
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
407 peptide sequences from a fasta file or a column in a tabular file
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
408
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
409 HLA alleles either entered as text or one per line in a text file
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
410
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
411
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
412 **OUTPUTS**
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
413
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
414 A tabular file containing the results returned from the IEDB web service
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
415
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
416 **Typical Workflow for Human MHC I Binding Prediction**
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
417
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
418 The RNAseq data for the subject would be used for:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
419
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
420 - HLA prediction by seq2HLA
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
421 - Novel Antigen Prediction by a variety of workflows to generate a Antigen peptide fasta
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
422
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
423
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
424 .. image:: $PATH_TO_IMAGES/IEDB_Workflow_QueryTabular.png
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
425 :width: 584
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
426 :height: 430
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
427
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
428 .. note:: The seq2HLA ClassI.HLAgenotype4digits output needs to be converted for IEDB alleles.
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
429
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
430 The seq2HLA ClassI.HLAgenotype4digits output:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
431
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
432 .. image:: $PATH_TO_IMAGES/seq2HLA_ClassI.HLAgenotype4digits.png
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
433 :width: 285
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
434 :height: 77
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
435
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
436 Needs to be converted into IEDB formatted alleles:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
437
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
438 .. image:: $PATH_TO_IMAGES/IEDB_formatted_alleles.png
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
439 :width: 74
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
440 :height: 81
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
441
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
442 In the workflow above QueryTabular tool converts the alleles:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
443
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
444 - Filter Dataset Input
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
445
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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446 * skip leading lines - *skip lines:* 1
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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447 * select columns - *columns:* 2,4
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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448 * regex replace value in column - *column:* 1 *regex pattern:* ^(\\w+[*]\\d\\d:\\d\\d\\d?).*$ *replacement expression:* HLA-\\1
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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449 * regex replace value in column - *column:* 2 *regex pattern:* ^(\\w+[*]\\d\\d:\\d\\d\\d?).*$ *replacement expression:* HLA-\\1
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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450
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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451 - SQL Query to generate tabular output
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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452
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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453 * SELECT c1 FROM t1 UNION SELECT c2 FROM t1
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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454
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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455
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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456 The IEDB formatting can also be performed by TextProcessing tools:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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457
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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458 .. image:: $PATH_TO_IMAGES/TextProcessingConversion.png
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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459 :width: 608
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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460 :height: 87
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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461
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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462 The TextProcessing steps to convert the alleles:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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463
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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464 - Remove beginning - removes the header line
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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465 - Replace Text - picks Allele 1 and Allele 2 from each line and reformats each on a separate line
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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466
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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467 * *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.*$
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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468 * *Replace with:* HLA-\\1\\nHLA-\\2
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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469
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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470 - Unique - remove duplicates
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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471
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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472
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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473 ]]></help>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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474 <citations>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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475 <citation type="doi">10.1093/nar/gku938</citation>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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476 </citations>
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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477 </tool>