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annotate pvacbind.xml @ 0:8184d4998259 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
author galaxyp
date Fri, 12 Dec 2025 16:49:12 +0000
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children 747d464670f9
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8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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1 <tool id="pvacbind" name="pVACbind" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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2 <description>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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3 The pVACbind tool of the pVACtools suite.
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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4 </description>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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5
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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6 <macros>
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7 <import>mhci_alleles_macros.xml</import>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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8 <import>mhcii_alleles_macros.xml</import>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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9 <import>alleles_macros.xml</import>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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10 <import>shared_macros.xml</import>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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11 </macros>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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12
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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13 <requirements>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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14 <container type="docker">griffithlab/pvactools:6.0.2</container>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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15 </requirements>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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16
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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17 <command><![CDATA[
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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18 @PREPARE_ALLELES_INPUT@
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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19 mkdir outputs &&
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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20 pvacbind run
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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21 '$input_file'
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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22 '$sample_name'
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23 #if $alleles.allelesrc == 'entry'
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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24 '$alleles_input'
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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25 #else
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26 \$(tr '\n' ',' < '$alleles.allele_file')
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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27 #end if
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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28 #for $algorithm in $algorithms
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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29 $algorithm
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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30 #end for
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31 outputs
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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32 --class-i-epitope-length $class_i_epitope_length
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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33 --class-ii-epitope-length $class_ii_epitope_length
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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34 #if $binding_threshold
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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35 --binding-threshold $binding_threshold
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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36 #end if
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37 #if $percentile_threshold_conditional.use_percentile_threshold == "true"
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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38 --percentile-threshold $percentile_threshold_conditional.percentile_threshold
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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39 --percentile-threshold-strategy $percentile_threshold_conditional.percentile_threshold_strategy
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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40 #end if
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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41 #if $allele_specific_binding_thresholds
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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42 --allele-specific-binding-thresholds
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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43 #end if
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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44 #if $top_score_metric != 'default'
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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45 --top-score-metric $top_score_metric
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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46 #end if
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47 #if $top_score_metric2 != 'default'
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48 --top-score-metric2 $top_score_metric2
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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49 #end if
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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50 #if $net_chop_method != 'default'
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51 --net-chop-method $net_chop_method
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52 #end if
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53 #if $netmhc_stab
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54 --netmhc-stab
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55 #end if
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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56 #if $net_chop_threshold
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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57 --net-chop-threshold $net_chop_threshold
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58 #end if
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59 #if $problematic_amino_acids != ''
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60 --problematic-amino-acids '$problematic_amino_acids'
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61 #end if
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62 #if $run_reference_proteome_similarity
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63 --run-reference-proteome-similarity
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64 #end if
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65 #if $blastp_db != 'default'
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66 --blastp-db $blastp_db
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67 #end if
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68 #if $peptide_fasta
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69 --peptide-fasta '$peptide_fasta'
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70 #end if
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71 #if $add_sample_name_reports_column
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72 --additional-report-columns sample_name
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73 #end if
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74 #if $exclude_NAs
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75 --exclude-NAs
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76 #end if
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77 #if $aggregate_inclusion_binding_threshold
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78 --aggregate-inclusion-binding-threshold $aggregate_inclusion_binding_threshold
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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79 #end if
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80 #if $aggregate_inclusion_count_limit
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81 --aggregate-inclusion-count-limit $aggregate_inclusion_count_limit
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82 #end if
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83 ]]></command>
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84
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85 <inputs>
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86 <expand macro="allele_inputs"/>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
87 <param name="input_file" type="data" format="fasta" optional="false" label="Input File"/>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
88 <param name="sample_name" type="text" optional="false" label="Sample Name">
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
89 <validator type="regex">^[a-zA-Z0-9_-]+$</validator>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
90 </param>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
91 <param name="algorithms" type="select" multiple="true" optional="false" label="Algorithm">
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
92 <option value="BigMHC_EL">BigMHC_EL</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
93 <option value="BigMHC_IM">BigMHC_IM</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
94 <option value="DeepImmuno">DeepImmuno</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
95 <option value="MHCflurry">MHCflurry</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
96 <option value="MHCflurryEL">MHCflurryEL</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
97 <option value="MHCnuggetsI">MHCnuggetsI</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
98 <option value="MHCnuggetsII">MHCnuggetsII</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
99 <option value="NNalign">NNalign</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
100 <option value="NetMHC">NetMHC</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
101 <option value="NetMHCIIpan">NetMHCIIpan</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
102 <option value="NetMHCIIpanEL">NetMHCIIpanEL</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
103 <option value="NetMHCcons">NetMHCcons</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
104 <option value="NetMHCpan">NetMHCpan</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
105 <option value="NetMHCpanEL">NetMHCpanEL</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
106 <option value="PickPocket">PickPocket</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
107 <option value="SMM">SMM</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
108 <option value="SMMPMBEC">SMMPMBEC</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
109 <option value="SMMalign">SMMalign</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
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110 <option value="all">all</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
111 <option value="all_class_i">all_class_i</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
112 <option value="all_class_ii">all_class_ii</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
113 </param>
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galaxyp
parents:
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114 <param argument="--class-i-epitope-length" type="select" multiple="true" optional="false" label="Class I Epitope Length">
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
115 <option value="8" selected="true">8</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
116 <option value="9" selected="true">9</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
117 <option value="10" selected="true">10</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
118 <option value="11" selected="true">11</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
119 <option value="12">12</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
120 <option value="13">13</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
121 <option value="14">14</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
122 <option value="15">15</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
123 </param>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
124 <param argument="--class-ii-epitope-length" type="select" multiple="true" optional="false" label="Class II Epitope Length">
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
125 <option value="11">11</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
126 <option value="12" selected="true">12</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
127 <option value="13" selected="true">13</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
128 <option value="14" selected="true">14</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
129 <option value="15" selected="true">15</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
130 <option value="16" selected="true">16</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
131 <option value="17" selected="true">17</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
132 <option value="18" selected="true">18</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
133 <option value="19">19</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
134 <option value="20">20</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
135 <option value="21">21</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
136 <option value="22">22</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
137 <option value="23">23</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
138 <option value="24">24</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
139 <option value="25">25</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
140 <option value="26">26</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
141 <option value="27">27</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
142 <option value="28">28</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
143 <option value="29">29</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
144 <option value="30">30</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
145 </param>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
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146 <param argument="--binding-threshold" type="integer" value="" optional="true" label="Binding Threshold"/>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
147 <conditional name="percentile_threshold_conditional">
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
148 <param name="use_percentile_threshold" type="select" label="Use Percentile Threshold">
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
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149 <option value="false" selected="true">No</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
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150 <option value="true">Yes</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
151 </param>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
152 <when value="true">
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
153 <param argument="--percentile-threshold" type="integer" optional="false" label="Percentile Threshold"/>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
154 <param argument="--percentile-threshold-strategy" type="select" label="Percentile Threshold Strategy">
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
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155 <option value="conservative" selected="true">conservative</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
156 <option value="exploratory">exploratory</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
157 </param>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
158 </when>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
159 <when value="false">
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
160 </when>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
161 </conditional>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
162 <param argument="--allele-specific-binding-thresholds" type="boolean" checked="false" label="Use allele-specific binding thresholds"/>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
163 <param argument="--top-score-metric" type="select" label="Top Score Metric">
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
164 <option value="default" selected="true">Use default</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
165 <option value="lowest">lowest</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
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166 <option value="median">median</option>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
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167 </param>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
diff changeset
168 <param argument="--top-score-metric2" type="select" label="Top Score Metric 2">
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
galaxyp
parents:
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169 <option value="default" selected="true">Use default</option>
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170 <option value="ic50">ic50</option>
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171 <option value="percentile">percentile</option>
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172 </param>
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173 <param argument="--net-chop-method" type="select" label="NetChop Prediction Method">
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174 <option value="default" selected="true">Use default</option>
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175 <option value="None">None</option>
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176 <option value="cterm">C term 3.0</option>
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177 <option value="20s">20S 3.0</option>
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178 </param>
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179 <param argument="--netmhc-stab" type="boolean" checked="false" label="Run NetMHCStabPan after all filtering and add stability predictions to predicted epitopes"/>
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180 <param argument="--net-chop-threshold" type="float" value="" optional="true" label="NetChop Prediction Threshold"/>
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181 <param argument="--problematic-amino-acids" type="text" value="" optional="true" label="Problematic Amino Acids">
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182 <validator type="regex">^@PROBLEM_AA_ARG_RE@$</validator>
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183 </param>
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184 <param argument="--run-reference-proteome-similarity" type="boolean" checked="false" label="Run reference proteome similarity"/>
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185 <param argument="--blastp-db" type="select" label="BlastP Database">
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186 <option value="default" selected="true">Use default</option>
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187 <option value="refseq_select_prot">refseq_select_prot</option>
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188 <option value="refseq_protein">refseq_protein</option>
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189 </param>
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190 <param argument="--peptide-fasta" type="data" format="fasta" optional="true" label="Peptide Fasta" help="When running the reference proteome similarity step, use this reference peptide FASTA file to find matches instead of blastp"/>
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191 <param name="add_sample_name_reports_column" argument="--additional-report-columns" type="boolean" checked="false" label="Add sample name reports column"/>
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192 <param argument="--exclude-NAs" type="boolean" checked="false" label="Exclude NA values from the filtered output"/>
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193 <param argument="--aggregate-inclusion-binding-threshold" type="integer" value="" optional="true" label="Aggregate Inclusion Binding Threshold"/>
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194 <param argument="--aggregate-inclusion-count-limit" type="integer" value="" optional="true" label="Aggregate Inclusion Binding Threshold"/>
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195 </inputs>
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196
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197 <outputs>
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198 <collection name="mhc_class_i_outputs" type="list" label="MHC Class I Outputs" >
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199 <discover_datasets pattern="(?P&lt;designation&gt;.+\.tsv)" ext="tabular" directory="outputs/MHC_Class_I"/>
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200 </collection>
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201 <collection name="mhc_class_ii_outputs" type="list" label="MHC Class II Outputs" >
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202 <discover_datasets pattern="(?P&lt;designation&gt;.+\.tsv)" ext="tabular" directory="outputs/MHC_Class_II"/>
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203 </collection>
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204 <collection name="combined_outputs" type="list" label="Combined Outputs" >
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205 <discover_datasets pattern="(?P&lt;designation&gt;.+\.tsv)" ext="tabular" directory="outputs/combined"/>
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206 </collection>
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207 </outputs>
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208
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209 <tests>
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210 <test expect_num_outputs="3">
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211 <param name="input_file" value="mhci/inputs/test.fasta" ftype="fasta"/>
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212 <param name="alleles|allele_file" value="mhci/inputs/test_alleles.txt" ftype="fasta"/>
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213 <param name="sample_name" value="pVACbind_mhci_test"/>
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214 <param name="algorithms" value="all"/>
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215 <param name="class_i_epitope_length" value="9,10,11"/>
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216 <param name="class_ii_epitope_length" value="12"/>
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217 <output_collection name="mhc_class_i_outputs" type="list">
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218 <element name="pVACbind_mhci_test.MHC_I.all_epitopes.aggregated.tsv" ftype="tabular">
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219 <assert_contents>
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220 <has_text text="ID&#x9;A*02:01&#x9;B*15:11&#x9;C*01:02&#x9;C*03:03&#x9;C*03:04"/>
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221 </assert_contents>
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222 </element>
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223 <element name="pVACbind_mhci_test.MHC_I.all_epitopes.tsv" ftype="tabular">
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224 <assert_contents>
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225 <has_text text="Mutation&#x9;HLA Allele&#x9;Sub-peptide Position&#x9;Epitope Seq"/>
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226 </assert_contents>
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227 </element>
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228 <element name="pVACbind_mhci_test.MHC_I.filtered.tsv" ftype="tabular">
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229 <assert_contents>
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230 <has_text text="Mutation&#x9;HLA Allele&#x9;Sub-peptide Position&#x9;Epitope Seq"/>
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231 </assert_contents>
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232 </element>
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233 </output_collection>
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234 </test>
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235 <test expect_num_outputs="3">
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236 <param name="input_file" value="mhcii/inputs/test.fasta" ftype="fasta"/>
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237 <param name="alleles|allele_file" value="mhcii/inputs/test_alleles.txt" ftype="fasta"/>
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238 <param name="sample_name" value="pVACbind_mhcii_test"/>
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239 <param name="algorithms" value="all"/>
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240 <param name="class_i_epitope_length" value="9"/>
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241 <param name="class_ii_epitope_length" value="12,13,14,15,16,17,18"/>
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242 <output_collection name="mhc_class_ii_outputs" type="list">
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243 <element name="pVACbind_mhcii_test.MHC_II.all_epitopes.aggregated.tsv" ftype="tabular">
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244 <assert_contents>
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245 <has_text text="ID&#x9;DPA1*01:03-DPB1*02:02&#x9;DQA1*01:01-DQB1*02:02&#x9;DRB1*01:02&#x9;DRB1*01:09"/>
8184d4998259 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit bec16bc8fc6f7c0dfc8b9739b1a40bcd68e21dac
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246 </assert_contents>
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247 </element>
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248 <element name="pVACbind_mhcii_test.MHC_II.all_epitopes.tsv" ftype="tabular">
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249 <assert_contents>
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250 <has_text text="Mutation&#x9;HLA Allele&#x9;Sub-peptide Position&#x9;Epitope Seq"/>
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251 </assert_contents>
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252 </element>
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253 <element name="pVACbind_mhcii_test.MHC_II.filtered.tsv" ftype="tabular">
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254 <assert_contents>
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255 <has_text text="Mutation&#x9;HLA Allele&#x9;Sub-peptide Position&#x9;Epitope Seq"/>
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256 </assert_contents>
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257 </element>
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258 </output_collection>
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259 </test>
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260 </tests>
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261
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262 <help><![CDATA[
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263 **pVACbind**
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264
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265 pVACbind, one component of the pVACtools_ software suite, identifies and prioritizes neoantigens in a FASTA file.
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266
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267 Required inputs are an input FASTA file, a sample name to be used in generated outputs, a list of alleles,
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268 epitope lengths, and finally a selection of epitope prediction algorithms.
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269
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270 Further usage details may be found in the pVACbind documentation_.
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271
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272 .. _pVACtools: https://pvactools.readthedocs.io/en/latest/index.html
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273 .. _documentation: https://pvactools.readthedocs.io/en/latest/pvacbind/run.html
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274 ]]></help>
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275
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276 <expand macro="citations"/>
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277 </tool>