# HG changeset patch # User galaxyp # Date 1745614671 0 # Node ID ee99ebe711a83d496383c5382fc5a6f14778b155 # Parent 42bc03ed02f6ead4fd6a156c5b78350230f107de planemo upload for repository https://unipept.ugent.be/apidocs commit 2f9f5541eeb65669ddb5ad74e8ba9fd437eea719 diff -r 42bc03ed02f6 -r ee99ebe711a8 unipept.py --- a/unipept.py Sat Jul 02 13:46:02 2022 +0000 +++ b/unipept.py Fri Apr 25 20:57:51 2025 +0000 @@ -558,6 +558,8 @@ post_data = [] if options.equate_il: post_data.append(('equate_il', 'true')) + else: + post_data.append(('equate_il', 'false')) if options.names or options.json: post_data.append(('extra', 'true')) post_data.append(('names', 'true')) diff -r 42bc03ed02f6 -r ee99ebe711a8 unipept.xml --- a/unipept.xml Sat Jul 02 13:46:02 2022 +0000 +++ b/unipept.xml Fri Apr 25 20:57:51 2025 +0000 @@ -1,4 +1,4 @@ - + retrieve taxonomy for peptides @@ -17,10 +17,10 @@ - + return the names in complete taxonomic lineage - + include fields for most specific taxonomic classification: taxon_rank,taxon_id,taxon_name before lineage @@ -39,13 +39,13 @@ + + unipept + python - - - - - - - - - - - - - - - - - - - Return the complete lineage of the taxonomic lowest common ancestor, and include ID fields. - - - - - - - Return the complete lineage of each organism, and include ID fields. - - - - - - - Return additional information fields: taxon_name, ec_references, go_references, refseq_ids, refseq_protein_ids, insdc_ids, insdc_protein_ids + + + + + + + + + + + + + + + Return the complete lineage of the taxonomic lowest common ancestor, and include ID fields. + + + + + + + Return the complete lineage of each organism, and include ID fields. + + + + + + + Return additional information fields: taxon_name, ec_references, go_references, refseq_ids, refseq_protein_ids, insdc_ids, insdc_protein_ids WARNING: Huge perfomance penalty! Only use for small number of peptides when the extra infomation is required. - - - - - - Return the name of the EC-number. + + + + + + Return the name of the EC-number. - - - - - - Return the name of the GO-term. + + + + + + Return the name of the GO-term. - - - - - - - Return the name of the GO-term. + + + + + + + Return the name of the GO-term. - - - - - - - Return the name of the EC-number and GO-term. + + + + + + + Return the name of the EC-number and GO-term. - - - - - - - Return the name of the EC-number and GO-term. + + + + + + + Return the name of the EC-number and GO-term. - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - - 'json' in selected_outputs and unipept['api'] in ('pept2lca', 'pept2taxa', 'peptinfo') - - - - - - 'ec_json' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo') - - - 'tsv' in selected_outputs - - - - - - - 'csv' in selected_outputs - - - 'ec_tsv' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo') - - - - - - 'go_tsv' in selected_outputs and unipept['api'] in ('pept2go', 'pept2funct', 'peptinfo') - - - - - - 'ipr_tsv' in selected_outputs and unipept['api'] in ('pept2interpro', 'pept2funct', 'peptinfo') - - - - - - - 'unmatched' in selected_outputs - - - - + + + + 'csv' in selected_outputs + + + 'ec_tsv' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo') + + + + + + 'go_tsv' in selected_outputs and unipept['api'] in ('pept2go', 'pept2funct', 'peptinfo') + + + + + + 'ipr_tsv' in selected_outputs and unipept['api'] in ('pept2interpro', 'pept2funct', 'peptinfo') + + + + + + 'unmatched' in selected_outputs + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - doi:10.1002/pmic.201400361 - - + + doi:10.1002/pmic.201400361 +