Mercurial > repos > galaxyp > iedb_netmhcpan

annotate netmhcpan.xml @ 0:88e44dab2988 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 12:56:30 +0000
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88e44dab2988 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_netmhcpan" name="NetMHCPan" version="4.1+galaxy0" profile="24.2">
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2 <description>MHC Binding prediction</description>
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3 <macros>
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4 <import>netmhcpan_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
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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11 <command detect_errors="exit_code"><![CDATA[
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12 #import re
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13 python '${__tool_directory__}/nextgen_iedb_api.py'
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14 --tool-group=mhci
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15 #for $method in $methods:
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16 --method=$method
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17 #end for
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18
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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19 #if $alleles.allelesrc == 'history':
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20 -A '$alleles.allele_file'
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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21 #else:
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22 -A '$entered_alleles'
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23 #end if
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24 -l '$length_start','$length_end'
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25
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26 #if $sequence.seqsrc == 'fasta':
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27 -i '$sequence.seq_fasta'
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28 #else if $sequence.seqsrc == 'tabular':
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29 -i '$sequence.seq_tsv'
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30 -c #echo int(str($sequence.pep_col)) - 1
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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31 #else:
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32 -i '$entered_seqs' -c 0
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33 #end if
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34 -o '$output'
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35 ]]></command>
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36 <configfiles>
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37 <expand macro="configfiles" />
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38 </configfiles>
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39 <inputs>
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40 <param name="methods" type="select" multiple="true" label="Prediction Method">
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41 <option value="netmhcpan_el" selected="true">netmhcpan_el</option>
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42 <option value="netmhcpan_ba">netmhcpan_ba</option>
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43 </param>
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44 <expand macro="inputs" hla_examples="HLA-A*03:01 HLA-B*07:02"/>
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45 </inputs>
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46 <outputs>
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47 <data name="output" format="tabular" label="IEDB NetMHCPan ${methods}"/>
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48 </outputs>
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49 <tests>
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50 <!-- test1 -->
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51 <test>
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52 <param name="alleles|allelesrc" value="entry"/>
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53 <param name="alleles|allele_text" value="HLA-A*01:01 HLA-A*03:01"/>
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54 <param name="methods" value="netmhcpan_ba,netmhcpan_el"/>
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55 <param name="sequence|seqsrc" value="entry"/>
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56 <param name="sequence|seq_text" value="SLYNTVATLYCVHQRIDV"/>
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57 <output name="output" file="outputs/netmhcpan_output_1.tsv"/>
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58 </test>
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59 <!-- test2 -->
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60 <test>
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61 <param name="alleles|allelesrc" value="history"/>
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62 <param name="alleles|allele_file" value="netmhcpan_alleles.txt"/>
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63 <param name="sequence|seqsrc" value="tabular"/>
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64 <param name="sequence|seq_tsv" value="seqs.tsv"/>
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65 <param name="sequence|pep_col" value="3"/>
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66 <output name="output" file="outputs/netmhcpan_output_2.tsv"/>
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67 </test>
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68 <!-- test3 -->
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69 <test>
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70 <param name="alleles|allelesrc" value="history"/>
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71 <param name="alleles|allele_file" value="netmhcpan_alleles.txt"/>
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72 <param name="length_start" value="8"/>
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73 <param name="length_end" value="14"/>
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74 <param name="sequence|seqsrc" value="fasta"/>
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75 <param name="sequence|seq_fasta" value="seqs.fa"/>
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76 <output name="output" file="outputs/netmhcpan_output_3.tsv"/>
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77 </test>
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78 </tests>
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79 <help><![CDATA[
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80 The NetMHCpan-4.1 server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs).
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81
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82 This tool uses the "Next-Generation IEDB Tools" API to submit NetMHCpan-4.1 jobs and retrieve results.
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83 IEDB is a free resource, funded by a contract from the National Institute of Allergy and Infectious Diseases.
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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84 ]]></help>
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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85 <citations>
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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86 <expand macro="citations" />
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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87 </citations>
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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88 </tool>