Mercurial > repos > galaxyp > iedb_netmhcpan

annotate netmhciipan.xml @ 0:4fb283cf23a5 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
author galaxyp
date Wed, 09 Jul 2025 12:56:02 +0000
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4fb283cf23a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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1 <tool id="iedb_netmhciipan" name="NetMHCiiPan" version="4.1+galaxy0" profile="24.2">
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2 <description>MHCii Binding prediction</description>
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3 <macros>
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4 <import>netmhciipan_alleles_macros.xml</import>
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5 <import>shared_macros.xml</import>
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6 </macros>
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7 <requirements>
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8 <expand macro="requirements" />
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9 </requirements>
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10
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11 <command detect_errors="exit_code"><![CDATA[
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12 #import re
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13
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14 python '${__tool_directory__}/nextgen_iedb_api.py'
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15 --tool-group=mhcii
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16 #for $method in $methods:
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17 --method=$method
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18 #end for
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19
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20 #if $alleles.allelesrc == 'history':
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21 -A '$alleles.allele_file'
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22 #else:
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23 -A '$entered_alleles'
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24 #end if
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25 #if $inversion == 'true'
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26 -R
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27 #end if
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28 -l '$length_start','$length_end'
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29 -P '$peptide_shift'
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30
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31 #if $sequence.seqsrc == 'fasta':
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32 -i '$sequence.seq_fasta'
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33 #else if $sequence.seqsrc == 'tabular':
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34 -i '$sequence.seq_tsv'
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35 -c #echo int(str($sequence.pep_col)) - 1
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36 #else:
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37 -i '$entered_seqs' -c 0
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38 #end if
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39
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40 -o '$output'
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41 ]]></command>
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42 <configfiles>
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43 <expand macro="configfiles" />
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44 </configfiles>
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45 <inputs>
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46 <param name="methods" type="select" multiple="true" label="prediction method">
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47 <option value="netmhciipan_el" selected="true">netmhciipan_el</option>
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48 <option value="netmhciipan_ba">netmhciipan_ba</option>
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49 </param>
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50 <expand macro="inputs" hla_examples="DPA1*01/DPB1*04:01 HLA-DRB1*01:01 H2-IAb"/>
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51 <param name="peptide_shift" type="integer" value="5" label="Peptide shift"/>
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52 <param name="inversion" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add reversed peptides to input database"/>
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53 </inputs>
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54 <outputs>
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55 <data name="output" format="tabular" label="IEDB NetMHCiiPan ${methods}"/>
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56 </outputs>
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57 <tests>
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58 <!-- test1 -->
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59 <test expect_num_outputs="1">
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60 <param name="alleles|allelesrc" value="entry"/>
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61 <param name="alleles|allele_text" value="HLA-DQA1*03:01/DQB1*06:02 HLA-DQA1*03:01/DQB1*06:04"/>
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62 <param name="methods" value="netmhciipan_ba,netmhciipan_el"/>
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63 <param name="length_start" value="13"/>
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64 <param name="length_end" value="17"/>
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65 <param name="sequence|seqsrc" value="entry"/>
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66 <param name="sequence|seq_text" value="SLYNTVATLYCVHQRIDV"/>
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67 <param name="inversion" value="true"/>
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68 <output name="output" file="outputs/netmhciipan_output_1.tsv"/>
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69 </test>
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70 <!-- test2 -->
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71 <test expect_num_outputs="1">
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72 <param name="alleles|allelesrc" value="history"/>
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73 <param name="alleles|allele_file" value="netmhciipan_alleles.txt"/>
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74 <param name="length_start" value="13"/>
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75 <param name="length_end" value="17"/>
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76 <param name="sequence|seqsrc" value="tabular"/>
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77 <param name="sequence|seq_tsv" value="seqs.tsv"/>
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78 <param name="sequence|pep_col" value="3"/>
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79 <param name="inversion" value="true"/>
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80 <output name="output" file="outputs/netmhciipan_output_2.tsv"/>
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81 </test>
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82 <!-- test3 -->
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83 <test expect_num_outputs="1">
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84 <param name="alleles|allelesrc" value="history"/>
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85 <param name="alleles|allele_file" value="netmhciipan_alleles.txt"/>
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86 <param name="length_start" value="13"/>
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87 <param name="length_end" value="17"/>
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88 <param name="peptide_shift" value="6"/>
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89 <param name="sequence|seqsrc" value="fasta"/>
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90 <param name="sequence|seq_fasta" value="seqs.fa"/>
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91 <param name="inversion" value="true"/>
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92 <output name="output" file="outputs/netmhciipan_output_3.tsv"/>
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93 </test>
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94 </tests>
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95 <help><![CDATA[
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96 The NetMHCiipan-4.1 server predicts binding of peptides to any MHC II molecule of known sequence using artificial neural networks (ANNs).
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97
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98 This tool uses the "Next-Generation IEDB Tools" API to submit NetMHCiipan-4.1 jobs and retrieve results.
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99 IEDB is a free resource, funded by a contract from the National Institute of Allergy and Infectious Diseases.
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100 ]]></help>
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101 <citations>
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102 <expand macro="citations" />
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103 </citations>
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104 </tool>