| Previous changeset 0:d2590ecc4189 (2021-03-16) Next changeset 2:41c7e03b3eab (2022-08-05) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b872ea086ebd98be64839e7bbb1ddf7a181943d0" |
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modified:
hamronize_tool.xml macros.xml |
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removed:
test-data/rgi/rgi.json test-data/summary.json |
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| diff -r d2590ecc4189 -r ec82fac4eb4b hamronize_tool.xml --- a/hamronize_tool.xml Tue Mar 16 12:38:42 2021 +0000 +++ b/hamronize_tool.xml Sat Oct 23 21:38:09 2021 +0000 |
| [ |
| @@ -1,9 +1,8 @@ -<tool id="hamronize_tool" name="hamronize" version="@VERSION@+galaxy0"> +<tool id="hamronize_tool" name="hamronize" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description> parse multiple Antimicrobial Resistance Analysis Reports into a common data structure</description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> <expand macro="version_command" /> @@ -34,7 +33,7 @@ ]]> </command> <inputs> - <param name="report" type="data" format="txt,tabular,tsv" label="Report file"/> + <param name="report" type="data" format="txt,tabular" label="Report file"/> <conditional name="select_tool"> <param name="tool" type="select" label="Tool"> <option value="abricate" selected="true">abricate</option> @@ -117,7 +116,7 @@ </inputs> <outputs> - <data format="tsv" name="output_tsv" label="${tool.name} on ${on_string}: Output" from_work_dir="hamronized.tsv"> + <data format="tabular" name="output_tsv" label="${tool.name} on ${on_string}: Output" from_work_dir="hamronized.tsv"> <filter>output_format == "tsv"</filter> </data> <data format="json" name="output_json" label="${tool.name} on ${on_string}: Output" from_work_dir="hamronized.json"> @@ -127,31 +126,31 @@ <tests> <!-- abricate --> <test expect_num_outputs="1"> - <param name="report" value="abricate/report.tsv" ftype="tsv" /> + <param name="report" value="abricate/report.tsv" ftype="tabular" /> <param name="tool" value="abricate" /> <param name="output_format" value="tsv" /> <param name="reference_database_version" value="db_v_1" /> <param name="analysis_software_version" value="tool_v_1" /> - <output name="output_tsv" ftype="tsv" file="hamronized_abricate.tsv" /> + <output name="output_tsv" file="hamronized_abricate.tsv" ftype="tabular" /> </test> <test expect_num_outputs="1"> - <param name="report" value="abricate/report.tsv" ftype="tsv" /> + <param name="report" value="abricate/report.tsv" ftype="tabular" /> <param name="tool" value="abricate" /> <param name="output_format" value="json" /> <param name="reference_database_version" value="db_v_1" /> <param name="analysis_software_version" value="tool_v_1" /> - <output name="output_json" ftype="json" file="hamronized_abricate.json" /> + <output name="output_json" file="hamronized_abricate.json" ftype="json" /> </test> <!-- ariba --> <test expect_num_outputs="1"> - <param name="report" value="ariba/report.tsv" ftype="tsv" /> + <param name="report" value="ariba/report.tsv" ftype="tabular" /> <param name="tool" value="ariba" /> <param name="output_format" value="tsv" /> <param name="reference_database_version" value="db_v_1" /> <param name="analysis_software_version" value="ariba_v1" /> <param name="input_file_name" value="ariba_report" /> <param name="reference_database_id" value="dbname" /> - <output name="output_tsv" ftype="tsv" file="hamronized_ariba.tsv" /> + <output name="output_tsv" file="hamronized_ariba.tsv" ftype="tabular" /> </test> <!-- rgi --> <test expect_num_outputs="1"> @@ -161,7 +160,7 @@ <param name="reference_database_version" value="card_v1" /> <param name="analysis_software_version" value="rgi_v1" /> <param name="input_file_name" value="rgi_report" /> - <output name="output_tsv" ftype="tsv" file="hamronized_rgi.tsv" /> + <output name="output_tsv" file="hamronized_rgi.tsv" ftype="tabular"/> </test> </tests> <help><![CDATA[ |
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| diff -r d2590ecc4189 -r ec82fac4eb4b macros.xml --- a/macros.xml Tue Mar 16 12:38:42 2021 +0000 +++ b/macros.xml Sat Oct 23 21:38:09 2021 +0000 |
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| @@ -1,9 +1,10 @@ <macros> - <token name="@VERSION@">1.0.3</token> + <token name="@TOOL_VERSION@">1.0.3</token> + <token name="@PROFILE@">20.05</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@VERSION@">hamronization</requirement> + <requirement type="package" version="@TOOL_VERSION@">hamronization</requirement> </requirements> </xml> |
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| diff -r d2590ecc4189 -r ec82fac4eb4b test-data/rgi/rgi.json --- a/test-data/rgi/rgi.json Tue Mar 16 12:38:42 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,1 +0,0 @@\n-{"NODE_1_length_803036_cov_42.265_33 # 30758 # 31933 # 1 # ID=1_33;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.599": {"gnl|BL_ORD_ID|2216|hsp_num:0": {"type_match": "Perfect", "model_id": "2399", "orf_strand": "+", "orf_start": 30758, "orf_end": 31933, "orf_from": "NODE_1_length_803036_cov_42.265_33", "model_name": "oqxA", "model_type": "protein homolog model", "model_type_id": 40292, "pass_evalue": "n/a", "pass_bitscore": "670", "ARO_accession": "3003922", "ARO_name": "oqxA", "ARO_category": {"36005": {"category_aro_accession": "0010004", "category_aro_cvterm_id": "36005", "category_aro_name": "resistance-nodulation-cell division (RND) antibiotic efflux pump", "category_aro_description": "Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding/hydrolysis but by proton movement down the transmembrane electrochemical gradient.", "category_aro_class_name": "AMR Gene Family"}, "35949": {"category_aro_accession": "0000030", "category_aro_cvterm_id": "35949", "category_aro_name": "tigecycline", "category_aro_description": "Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.", "category_aro_class_name": "Antibiotic"}, "35954": {"category_aro_accession": "0000036", "category_aro_cvterm_id": "35954", "category_aro_name": "ciprofloxacin", "category_aro_description": "Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.", "category_aro_class_name": "Antibiotic"}, "35992": {"category_aro_accession": "0000075", "category_aro_cvterm_id": "35992", "category_aro_name": "nitrofurantoin", "category_aro_description": "Nitrofurantoin is an antibiotic used to treat urinary tract infections. It inhibits enzyme synthesis by inhibiting essential enzymes involved in the citric acid cycle, as well as those involved in DNA, RNA, and protein synthesis. It is marketed under the following brand names: Furadantin, Macrobid, Macrodantin, Nitro Macro and Urantoin.", "category_aro_class_name": "Antibiotic"}, "36327": {"category_aro_accession": "3000188", "category_aro_cvterm_id": "36327", "category_aro_name": "trimethoprim", "category_aro_description": "Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.", "category_aro_class_name": "Antibiotic"}, "35920": {"category_aro_accession": "0000001", "category_aro_cvterm_id": "35920", "category_aro_name": "fluoroquinolone antibiotic", "category_aro_description": "The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.", "category_aro_class_name": "Drug Class"}, "35960": {"category_aro_accession": "0000042", "category_aro_cvterm_id": "35960", "category_aro_name": "glycylcycline", "category_aro_description": "Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inh'..b'ng the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.", "category_aro_class_name": "Drug Class"}, "36526": {"category_aro_accession": "3000387", "category_aro_cvterm_id": "36526", "category_aro_name": "phenicol antibiotic", "category_aro_description": "Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.", "category_aro_class_name": "Drug Class"}, "37250": {"category_aro_accession": "3000870", "category_aro_cvterm_id": "37250", "category_aro_name": "triclosan", "category_aro_description": "Triclosan is a common antibacterial agent added to many consumer products as a biocide. It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).", "category_aro_class_name": "Drug Class"}, "36298": {"category_aro_accession": "3000159", "category_aro_cvterm_id": "36298", "category_aro_name": "efflux pump complex or subunit conferring antibiotic resistance", "category_aro_description": "Efflux proteins that pump antibiotic out of a cell to confer resistance.", "category_aro_class_name": "Efflux Component"}, "36590": {"category_aro_accession": "3000451", "category_aro_cvterm_id": "36590", "category_aro_name": "protein(s) and two-component regulatory system modulating antibiotic efflux", "category_aro_description": "Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.", "category_aro_class_name": "Efflux Regulator"}, "35997": {"category_aro_accession": "0001001", "category_aro_cvterm_id": "35997", "category_aro_name": "antibiotic target alteration", "category_aro_description": "Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.", "category_aro_class_name": "Resistance Mechanism"}, "36001": {"category_aro_accession": "0010000", "category_aro_cvterm_id": "36001", "category_aro_name": "antibiotic efflux", "category_aro_description": "Antibiotic resistance via the transport of antibiotics out of the cell.", "category_aro_class_name": "Resistance Mechanism"}}, "evalue": 2.11739, "max_identities": 14, "bit_score": 23.483, "cvterm_id": "36849", "query": "TLKELAEAAGVSKATLHRFCGTRDNLVQMLEDHGETVLNQIIQACDLEH-----AEPLEALQRLI", "match": "+L E+A+AAGV++ ++ + +L + + E+ + ++ +LE+ +PL L+ ++", "sequence_from_db": "SLGEIAKAAGVTRGAIYWHFKDKSDLFSEIWELSESNIGEL----ELEYQAKFPGDPLSVLREIL", "sequence_from_broadstreet": "MARKTKQEAQETRQHILDVALRLFSQQGVSSTSLGEIAKAAGVTRGAIYWHFKDKSDLFSEIWELSESNIGELELEYQAKFPGDPLSVLREILIHVLESTVTEERRRLLMEIIFHKCEFVGEMAVVQQAQRNLCLESYDRIEQTLKHCIEAKMLPADLMTRRAAIIMRGYISGLMENWLFAPQSFDLKKEARDYVAILLEMYLLCPTLRNPATNE", "dna_sequence_from_broadstreet": "ATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCGTTACGCGCGGTGCAATCTACTGGCATTTTAAAGACAAGTCGGATTTGTTCAGTGAGATCTGGGAACTGTCAGAATCCAATATTGGTGAACTAGAGCTTGAGTATCAGGCAAAATTCCCTGGCGATCCACTCTCAGTATTAAGAGAGATATTAATTCATGTTCTTGAATCCACGGTGACAGAAGAACGGCGTCGATTATTGATGGAGATTATATTCCACAAATGCGAATTTGTCGGAGAAATGGCTGTTGTGCAACAGGCACAACGTAATCTCTGTCTGGAAAGTTATGACCGTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATATTTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCTGTGCCCCACGCTTCGTAATCCTGCCACTAACGAATAA", "partial": "0", "query_start": 73, "query_end": 252, "orf_dna_sequence": "ATGACCCTGATTTCCCATGACGAGCGACTCATCAAGGCGCTGGCAGTCGCTATCGTCGACCGCCCACGAGCGACGCTGAAGGAACTGGCCGAGGCGGCCGGCGTAAGCAAGGCCACCCTGCACCGCTTCTGCGGCACGCGGGACAACCTGGTGCAGATGCTCGAGGACCACGGAGAGACCGTACTGAACCAGATCATCCAGGCCTGCGACCTGGAGCATGCCGAGCCTCTGGAGGCGTTGCAGCGCCTGATCAAGGAACACCTCACCCAC", "orf_prot_sequence": "MTLISHDERLIKALAVAIVDRPRATLKELAEAAGVSKATLHRFCGTRDNLVQMLEDHGETVLNQIIQACDLEHAEPLEALQRLIKEHLTH", "perc_identity": 21.54}}}\n\\ No newline at end of file\n' |
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| diff -r d2590ecc4189 -r ec82fac4eb4b test-data/summary.json --- a/test-data/summary.json Tue Mar 16 12:38:42 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1 +0,0 @@\n-[{"input_file_name":"GCF_010120755.1_ASM1012075v1_genomic","gene_symbol":"aacA-ENT1","gene_name":"aminoglycoside 6\'-N-acetyltransferase","reference_database_id":"ncbi","reference_database_version":"db_v_1","reference_accession":"NG_052371.1","analysis_software_name":"abricate","analysis_software_version":"tool_v_1","sequence_identity":100.0,"input_sequence_id":"NZ_CP039729.1","input_protein_start":"","input_protein_stop":"","input_gene_start":2163439,"input_gene_stop":2163987,"reference_protein_start":"","reference_protein_stop":"","reference_gene_start":"","reference_gene_stop":"","strand_orientation":"-","coverage_depth":"","coverage_percentage":100.0,"coverage_ratio":"","reference_gene_length":"","reference_protein_length":"","input_gene_length":"","input_protein_length":"","drug_class":"AMINOGLYCOSIDE","antimicrobial_agent":"","resistance_mechanism":""},{"input_file_name":"GCF_010120755.1_ASM1012075v1_genomic","gene_symbol":"aacA-ENT1","gene_name":"aminoglycoside 6\'-N-acetyltransferase","reference_database_id":"ncbi","reference_database_version":"db_v_1","reference_accession":"NG_052371.1","analysis_software_name":"abricate","analysis_software_version":"tool_v_1","sequence_identity":100.0,"input_sequence_id":"NZ_CP039729.1","input_protein_start":null,"input_protein_stop":null,"input_gene_start":2163439,"input_gene_stop":2163987,"reference_protein_start":null,"reference_protein_stop":null,"reference_gene_start":null,"reference_gene_stop":null,"strand_orientation":"-","coverage_depth":null,"coverage_percentage":100.0,"coverage_ratio":null,"reference_gene_length":null,"reference_protein_length":null,"input_gene_length":null,"input_protein_length":null,"drug_class":"AMINOGLYCOSIDE","antimicrobial_agent":null,"resistance_mechanism":null},{"input_file_name":"GCF_010120755.1_ASM1012075v1_genomic","gene_symbol":"eat(A)","gene_name":"ABC-F type ribosomal protection protein Eat(A)","reference_database_id":"ncbi","reference_database_version":"db_v_1","reference_accession":"NG_047762.1","analysis_software_name":"abricate","analysis_software_version":"tool_v_1","sequence_identity":100.0,"input_sequence_id":"NZ_CP039729.1","input_protein_start":"","input_protein_stop":"","input_gene_start":656118,"input_gene_stop":657620,"reference_protein_start":"","reference_protein_stop":"","reference_gene_start":"","reference_gene_stop":"","strand_orientation":"+","coverage_depth":"","coverage_percentage":100.0,"coverage_ratio":"","reference_gene_length":"","reference_protein_length":"","input_gene_length":"","input_protein_length":"","drug_class":"PLEUROMUTILIN","antimicrobial_agent":"","resistance_mechanism":""},{"input_file_name":"GCF_010120755.1_ASM1012075v1_genomic","gene_symbol":"eat(A)","gene_name":"ABC-F type ribosomal protection protein Eat(A)","reference_database_id":"ncbi","reference_database_version":"db_v_1","reference_accession":"NG_047762.1","analysis_software_name":"abricate","analysis_software_version":"tool_v_1","sequence_identity":100.0,"input_sequence_id":"NZ_CP039729.1","input_protein_start":null,"input_protein_stop":null,"input_gene_start":656118,"input_gene_stop":657620,"reference_protein_start":null,"reference_protein_stop":null,"reference_gene_start":null,"reference_gene_stop":null,"strand_orientation":"+","coverage_depth":null,"coverage_percentage":100.0,"coverage_ratio":null,"reference_gene_length":null,"reference_protein_length":null,"input_gene_length":null,"input_protein_length":null,"drug_class":"PLEUROMUTILIN","antimicrobial_agent":null,"resistance_mechanism":null},{"input_file_name":"GCF_010120755.1_ASM1012075v1_genomic","gene_symbol":"msr(C)","gene_name":"ABC-F type ribosomal protection protein Msr(C)","reference_database_id":"ncbi","reference_database_version":"db_v_1","reference_accession":"NG_048003.1","analysis_software_name":"abricate","analysis_software_version":"tool_v_1","sequence_identity":98.92,"input_sequence_id":"NZ_CP039729.1","input_protein_start":"","input_protein_stop":"","input_gen'..b'eference_gene_stop":null,"strand_orientation":"+","coverage_depth":null,"coverage_percentage":100.0,"coverage_ratio":null,"reference_gene_length":null,"reference_protein_length":null,"input_gene_length":null,"input_protein_length":null,"drug_class":"fluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic","antimicrobial_agent":null,"resistance_mechanism":"antibiotic efflux"},{"input_file_name":"rgi_report","gene_symbol":"rmtC","gene_name":"16S rRNA methyltransferase (G1405)","reference_database_id":"CARD","reference_database_version":"card_v1","reference_accession":3000861,"analysis_software_name":"rgi","analysis_software_version":"rgi_v1","sequence_identity":100.0,"input_sequence_id":"NODE_40_length_7360_cov_24.8738_6","input_protein_start":"","input_protein_stop":"","input_gene_start":6358,"input_gene_stop":7203,"reference_protein_start":"","reference_protein_stop":"","reference_gene_start":"","reference_gene_stop":"","strand_orientation":"-","coverage_depth":"","coverage_percentage":100.0,"coverage_ratio":"","reference_gene_length":"","reference_protein_length":"","input_gene_length":"","input_protein_length":"","drug_class":"aminoglycoside antibiotic","antimicrobial_agent":"","resistance_mechanism":"antibiotic target alteration"},{"input_file_name":"rgi_report","gene_symbol":"rmtC","gene_name":"16S rRNA methyltransferase (G1405)","reference_database_id":"CARD","reference_database_version":"card_v1","reference_accession":3000861,"analysis_software_name":"rgi","analysis_software_version":"rgi_v1","sequence_identity":100.0,"input_sequence_id":"NODE_40_length_7360_cov_24.8738_6","input_protein_start":null,"input_protein_stop":null,"input_gene_start":6358,"input_gene_stop":7203,"reference_protein_start":null,"reference_protein_stop":null,"reference_gene_start":null,"reference_gene_stop":null,"strand_orientation":"-","coverage_depth":null,"coverage_percentage":100.0,"coverage_ratio":null,"reference_gene_length":null,"reference_protein_length":null,"input_gene_length":null,"input_protein_length":null,"drug_class":"aminoglycoside antibiotic","antimicrobial_agent":null,"resistance_mechanism":"antibiotic target alteration"},{"input_file_name":"rgi_report","gene_symbol":"sul1","gene_name":"sulfonamide resistant sul","reference_database_id":"CARD","reference_database_version":"card_v1","reference_accession":3000410,"analysis_software_name":"rgi","analysis_software_version":"rgi_v1","sequence_identity":100.0,"input_sequence_id":"NODE_57_length_1134_cov_34.8908_1","input_protein_start":"","input_protein_stop":"","input_gene_start":25,"input_gene_stop":864,"reference_protein_start":"","reference_protein_stop":"","reference_gene_start":"","reference_gene_stop":"","strand_orientation":"-","coverage_depth":"","coverage_percentage":100.0,"coverage_ratio":"","reference_gene_length":"","reference_protein_length":"","input_gene_length":"","input_protein_length":"","drug_class":"sulfonamide antibiotic","antimicrobial_agent":"","resistance_mechanism":"antibiotic target replacement"},{"input_file_name":"rgi_report","gene_symbol":"sul1","gene_name":"sulfonamide resistant sul","reference_database_id":"CARD","reference_database_version":"card_v1","reference_accession":3000410,"analysis_software_name":"rgi","analysis_software_version":"rgi_v1","sequence_identity":100.0,"input_sequence_id":"NODE_57_length_1134_cov_34.8908_1","input_protein_start":null,"input_protein_stop":null,"input_gene_start":25,"input_gene_stop":864,"reference_protein_start":null,"reference_protein_stop":null,"reference_gene_start":null,"reference_gene_stop":null,"strand_orientation":"-","coverage_depth":null,"coverage_percentage":100.0,"coverage_ratio":null,"reference_gene_length":null,"reference_protein_length":null,"input_gene_length":null,"input_protein_length":null,"drug_class":"sulfonamide antibiotic","antimicrobial_agent":null,"resistance_mechanism":"antibiotic target replacement"}]\n\\ No newline at end of file\n' |