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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit 2727330d0394c8a1f178061abffe91fe621be7ee
| author | galaxyp |
|---|---|
| date | Fri, 12 Dec 2025 21:10:38 +0000 |
| parents | 8184d4998259 |
| children |
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<tool id="pvacbind" name="pVACbind" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2"> <description> The pVACbind tool of the pVACtools suite. </description> <macros> <import>mhci_alleles_macros.xml</import> <import>mhcii_alleles_macros.xml</import> <import>alleles_macros.xml</import> <import>shared_macros.xml</import> </macros> <requirements> <container type="docker">griffithlab/pvactools:6.0.2</container> </requirements> <command><![CDATA[ @PREPARE_ALLELES_INPUT@ mkdir outputs && pvacbind run '$input_file' '$sample_name' #if $alleles.allelesrc == 'entry' '$alleles_input' #else \$(tr '\n' ',' < '$alleles.allele_file') #end if #for $algorithm in $algorithms $algorithm #end for outputs --class-i-epitope-length $class_i_epitope_length --class-ii-epitope-length $class_ii_epitope_length #if $binding_threshold --binding-threshold $binding_threshold #end if #if $percentile_threshold --percentile-threshold $percentile_threshold #end if #if $percentile_threshold_strategy != 'default' --percentile-threshold-strategy $percentile_threshold_strategy #end if #if $allele_specific_binding_thresholds --allele-specific-binding-thresholds #end if #if $top_score_metric != 'default' --top-score-metric $top_score_metric #end if #if $top_score_metric2 != 'default' --top-score-metric2 $top_score_metric2 #end if #if $net_chop_method != 'default' --net-chop-method $net_chop_method #end if #if $netmhc_stab --netmhc-stab #end if #if $net_chop_threshold --net-chop-threshold $net_chop_threshold #end if #if $problematic_amino_acids != '' --problematic-amino-acids '$problematic_amino_acids' #end if #if $run_reference_proteome_similarity --run-reference-proteome-similarity #end if #if $blastp_db != 'default' --blastp-db $blastp_db #end if #if $peptide_fasta --peptide-fasta '$peptide_fasta' #end if #if $add_sample_name_reports_column --additional-report-columns sample_name #end if #if $exclude_NAs --exclude-NAs #end if #if $aggregate_inclusion_binding_threshold --aggregate-inclusion-binding-threshold $aggregate_inclusion_binding_threshold #end if #if $aggregate_inclusion_count_limit --aggregate-inclusion-count-limit $aggregate_inclusion_count_limit #end if ]]></command> <inputs> <expand macro="allele_inputs"/> <param name="input_file" type="data" format="fasta" optional="false" label="Input File"/> <param name="sample_name" type="text" optional="false" label="Sample Name"> <validator type="regex">^[a-zA-Z0-9_-]+$</validator> </param> <param name="algorithms" type="select" multiple="true" optional="false" label="Algorithm"> <option value="BigMHC_EL">BigMHC_EL</option> <option value="BigMHC_IM">BigMHC_IM</option> <option value="DeepImmuno">DeepImmuno</option> <option value="MHCflurry">MHCflurry</option> <option value="MHCflurryEL">MHCflurryEL</option> <option value="MHCnuggetsI">MHCnuggetsI</option> <option value="MHCnuggetsII">MHCnuggetsII</option> <option value="NNalign">NNalign</option> <option value="NetMHC">NetMHC</option> <option value="NetMHCIIpan">NetMHCIIpan</option> <option value="NetMHCIIpanEL">NetMHCIIpanEL</option> <option value="NetMHCcons">NetMHCcons</option> <option value="NetMHCpan">NetMHCpan</option> <option value="NetMHCpanEL">NetMHCpanEL</option> <option value="PickPocket">PickPocket</option> <option value="SMM">SMM</option> <option value="SMMPMBEC">SMMPMBEC</option> <option value="SMMalign">SMMalign</option> <option value="all">all</option> <option value="all_class_i">all_class_i</option> <option value="all_class_ii">all_class_ii</option> </param> <param argument="--class-i-epitope-length" type="select" multiple="true" optional="false" label="Class I Epitope Length"> <option value="8" selected="true">8</option> <option value="9" selected="true">9</option> <option value="10" selected="true">10</option> <option value="11" selected="true">11</option> <option value="12">12</option> <option value="13">13</option> <option value="14">14</option> <option value="15">15</option> </param> <param argument="--class-ii-epitope-length" type="select" multiple="true" optional="false" label="Class II Epitope Length"> <option value="11">11</option> <option value="12" selected="true">12</option> <option value="13" selected="true">13</option> <option value="14" selected="true">14</option> <option value="15" selected="true">15</option> <option value="16" selected="true">16</option> <option value="17" selected="true">17</option> <option value="18" selected="true">18</option> <option value="19">19</option> <option value="20">20</option> <option value="21">21</option> <option value="22">22</option> <option value="23">23</option> <option value="24">24</option> <option value="25">25</option> <option value="26">26</option> <option value="27">27</option> <option value="28">28</option> <option value="29">29</option> <option value="30">30</option> </param> <param argument="--binding-threshold" type="integer" value="" optional="true" label="Binding Threshold"/> <param argument="--percentile-threshold" type="float" value="" optional="true" label="Percentile Threshold"/> <param argument="--percentile-threshold-strategy" type="select" label="Percentile Threshold Strategy"> <option value="default" selected="true">Use default</option> <option value="conservative">conservative</option> <option value="exploratory">exploratory</option> </param> <param argument="--allele-specific-binding-thresholds" type="boolean" checked="false" label="Use allele-specific binding thresholds"/> <param argument="--top-score-metric" type="select" label="Top Score Metric"> <option value="default" selected="true">Use default</option> <option value="lowest">lowest</option> <option value="median">median</option> </param> <param argument="--top-score-metric2" type="select" label="Top Score Metric 2"> <option value="default" selected="true">Use default</option> <option value="ic50">ic50</option> <option value="percentile">percentile</option> </param> <param argument="--net-chop-method" type="select" label="NetChop Prediction Method"> <option value="default" selected="true">Use default</option> <option value="None">None</option> <option value="cterm">C term 3.0</option> <option value="20s">20S 3.0</option> </param> <param argument="--netmhc-stab" type="boolean" checked="false" label="Run NetMHCStabPan after all filtering and add stability predictions to predicted epitopes"/> <param argument="--net-chop-threshold" type="float" value="" optional="true" label="NetChop Prediction Threshold"/> <param argument="--problematic-amino-acids" type="text" value="" optional="true" label="Problematic Amino Acids"> <validator type="regex">^@PROBLEM_AA_ARG_RE@$</validator> </param> <param argument="--run-reference-proteome-similarity" type="boolean" checked="false" label="Run reference proteome similarity"/> <param argument="--blastp-db" type="select" label="BlastP Database"> <option value="default" selected="true">Use default</option> <option value="refseq_select_prot">refseq_select_prot</option> <option value="refseq_protein">refseq_protein</option> </param> <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"/> <param name="add_sample_name_reports_column" argument="--additional-report-columns" type="boolean" checked="false" label="Add sample name reports column"/> <param argument="--exclude-NAs" type="boolean" checked="false" label="Exclude NA values from the filtered output"/> <param argument="--aggregate-inclusion-binding-threshold" type="integer" value="" optional="true" label="Aggregate Inclusion Binding Threshold"/> <param argument="--aggregate-inclusion-count-limit" type="integer" value="" optional="true" label="Aggregate Inclusion Count Limit"/> </inputs> <outputs> <collection name="mhc_class_i_outputs" type="list" label="MHC Class I Outputs" > <discover_datasets pattern="(?P<designation>.+\.tsv)" ext="tabular" directory="outputs/MHC_Class_I"/> </collection> <collection name="mhc_class_ii_outputs" type="list" label="MHC Class II Outputs" > <discover_datasets pattern="(?P<designation>.+\.tsv)" ext="tabular" directory="outputs/MHC_Class_II"/> </collection> <collection name="combined_outputs" type="list" label="Combined Outputs" > <discover_datasets pattern="(?P<designation>.+\.tsv)" ext="tabular" directory="outputs/combined"/> </collection> </outputs> <tests> <test expect_num_outputs="3"> <param name="input_file" value="mhci/inputs/test.fasta" ftype="fasta"/> <param name="alleles|allele_file" value="mhci/inputs/test_alleles.txt" ftype="fasta"/> <param name="sample_name" value="pVACbind_mhci_test"/> <param name="algorithms" value="all"/> <param name="class_i_epitope_length" value="9,10,11"/> <param name="class_ii_epitope_length" value="12"/> <output_collection name="mhc_class_i_outputs" type="list"> <element name="pVACbind_mhci_test.MHC_I.all_epitopes.aggregated.tsv" ftype="tabular"> <assert_contents> <has_text text="ID	A*02:01	B*15:11	C*01:02	C*03:03	C*03:04"/> </assert_contents> </element> <element name="pVACbind_mhci_test.MHC_I.all_epitopes.tsv" ftype="tabular"> <assert_contents> <has_text text="Mutation	HLA Allele	Sub-peptide Position	Epitope Seq"/> </assert_contents> </element> <element name="pVACbind_mhci_test.MHC_I.filtered.tsv" ftype="tabular"> <assert_contents> <has_text text="Mutation	HLA Allele	Sub-peptide Position	Epitope Seq"/> </assert_contents> </element> </output_collection> </test> <test expect_num_outputs="3"> <param name="input_file" value="mhcii/inputs/test.fasta" ftype="fasta"/> <param name="alleles|allele_file" value="mhcii/inputs/test_alleles.txt" ftype="fasta"/> <param name="sample_name" value="pVACbind_mhcii_test"/> <param name="algorithms" value="all"/> <param name="class_i_epitope_length" value="9"/> <param name="class_ii_epitope_length" value="12,13,14,15,16,17,18"/> <output_collection name="mhc_class_ii_outputs" type="list"> <element name="pVACbind_mhcii_test.MHC_II.all_epitopes.aggregated.tsv" ftype="tabular"> <assert_contents> <has_text text="ID	DPA1*01:03-DPB1*02:02	DQA1*01:01-DQB1*02:02	DRB1*01:02	DRB1*01:09"/> </assert_contents> </element> <element name="pVACbind_mhcii_test.MHC_II.all_epitopes.tsv" ftype="tabular"> <assert_contents> <has_text text="Mutation	HLA Allele	Sub-peptide Position	Epitope Seq"/> </assert_contents> </element> <element name="pVACbind_mhcii_test.MHC_II.filtered.tsv" ftype="tabular"> <assert_contents> <has_text text="Mutation	HLA Allele	Sub-peptide Position	Epitope Seq"/> </assert_contents> </element> </output_collection> </test> </tests> <help><![CDATA[ **pVACbind** pVACbind, one component of the pVACtools_ software suite, identifies and prioritizes neoantigens in a FASTA file. Required inputs are an input FASTA file, a sample name to be used in generated outputs, a list of alleles, epitope lengths, and finally a selection of epitope prediction algorithms. Further usage details may be found in the pVACbind documentation_. .. _pVACtools: https://pvactools.readthedocs.io/en/latest/index.html .. _documentation: https://pvactools.readthedocs.io/en/latest/pvacbind/run.html ]]></help> <expand macro="citations"/> </tool>