# HG changeset patch # User bgruening # Date 1657017458 0 # Node ID bc88856eddab98514aea2cfccde494a3c8556610 # Parent e78e25d3b4bde537979c5bbd2785dc6b9855361a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit dc45770442ff516d6f3733e4bdb284be3163de67 diff -r e78e25d3b4bd -r bc88856eddab antismash.xml --- a/antismash.xml Tue May 31 14:04:07 2022 +0000 +++ b/antismash.xml Tue Jul 05 10:37:38 2022 +0000 @@ -23,6 +23,13 @@ ln -s $genefinding_gff3 annotation.gff3 && #end if + #if $sideload.file + #if $sideload.format == 'harmonize' + python '$__tool_directory__/harmonize2antismash.py' '$sideload.file' sideload.json && + #else + ln -s '$sideload.file' sideload.json && + #end if + #end if ## create html folder mkdir -p '$htmloutputfolder' && @@ -62,6 +69,10 @@ --rre-cutoff $advanced_options.rre_cutoff --rre-minlength $advanced_options.rre_minlength + #if $sideload.file + --sideload 'sideload.json' + #end if + input_tempfile.$file_extension && ## copy all content to html folder @@ -149,6 +160,14 @@ +
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+ @@ -236,6 +255,23 @@ + + +
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+ + 6.1.1 - 0 + 1 antismash diff -r e78e25d3b4bd -r bc88856eddab test-data/harmonize.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/harmonize.json Tue Jul 05 10:37:38 2022 +0000 @@ -0,0 +1,64 @@ +[ + { + "input_file_name": "ARBH01000003.1", + "gene_symbol": "mecA_6", + "gene_name": "mecA", + "reference_database_id": "resfinder", + "reference_database_version": 1, + "reference_accession": "BX571856", + "analysis_software_name": "abricate", + "analysis_software_version": 0.5, + "sequence_identity": 100, + "input_sequence_id": "ARBH01000003.1", + "input_protein_start": null, + "input_protein_stop": null, + "input_gene_start": 2, + "input_gene_stop": 3500, + "reference_protein_start": null, + "reference_protein_stop": null, + "reference_gene_start": null, + "reference_gene_stop": null, + "strand_orientation": "-", + "coverage_depth": null, + "coverage_percentage": 100, + "coverage_ratio": null, + "reference_gene_length": null, + "reference_protein_length": null, + "input_gene_length": null, + "input_protein_length": null, + "drug_class": "Amoxicillin;Amoxicillin+Clavulanic_acid;Ampicillin;Ampicillin+Clavulanic_acid;Cefepime;Cefixime;Cefotaxime;Cefoxitin;Ceftazidime;Ertapenem;Imipenem;Meropenem;Piperacillin;Piperacillin+Tazobactam", + "antimicrobial_agent": null, + "resistance_mechanism": null + }, + { + "input_file_name": "ARBH01000003.1", + "gene_symbol": "mecA", + "gene_name": "mecA", + "reference_database_id": "resfinder", + "reference_database_version": 1, + "reference_accession": "BX571856", + "analysis_software_name": "staramr", + "analysis_software_version": 0.5, + "sequence_identity": 100, + "input_sequence_id": "ARBH01000003.1", + "input_protein_start": null, + "input_protein_stop": null, + "input_gene_start": 2, + "input_gene_stop": 3500, + "reference_protein_start": null, + "reference_protein_stop": null, + "reference_gene_start": null, + "reference_gene_stop": null, + "strand_orientation": null, + "coverage_depth": null, + "coverage_percentage": 100, + "coverage_ratio": 1, + "reference_gene_length": null, + "reference_protein_length": null, + "input_gene_length": null, + "input_protein_length": null, + "drug_class": "unknown[mecA_6_BX571856]", + "antimicrobial_agent": null, + "resistance_mechanism": null + } +] diff -r e78e25d3b4bd -r bc88856eddab test-data/index.4.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/index.4.html Tue Jul 05 10:37:38 2022 +0000 @@ -0,0 +1,459 @@ + + + + + + input_tempfile - 1 region(s) - antiSMASH results + + + + + + + + + + + + + + + + + + + +
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Identified secondary metabolite regions using strictness 'relaxed'

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RegionTypeFromToMost similar known clusterSimilarity
+ Region 1 + + + T1PKS,bht + 13,500
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+ If you have found antiSMASH useful, please cite us. +
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+ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff -r e78e25d3b4bd -r bc88856eddab test-data/index.5.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/index.5.html Tue Jul 05 10:37:38 2022 +0000 @@ -0,0 +1,459 @@ + + + + + + input_tempfile - 1 region(s) - antiSMASH results + + + + + + + + + + + + + + + + + + + +
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Identified secondary metabolite regions using strictness 'relaxed'

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RegionTypeFromToMost similar known clusterSimilarity
+ Region 1 + + + T1PKS + 13,500
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+ If you have found antiSMASH useful, please cite us. +
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+ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff -r e78e25d3b4bd -r bc88856eddab test-data/sideload.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sideload.json Tue Jul 05 10:37:38 2022 +0000 @@ -0,0 +1,40 @@ +{ + "tool": { + "name": "Example tool", + "version": "1.2.3", + "description": "Example of external result sideloading in antiSMASH", + "configuration": { + "verbose": "true", + "multisetting": [ + "first", + "second" + ] + } + }, + "records": [ + { + "name": "ARBH01000003.1", + "subregions": [ + { + "start": 2, + "end": 3500, + "label": "dhpg biosynthesis", + "details": { + "score": "6.5" + } + } + ], + "protoclusters": [ + { + "core_start": 2, + "core_end": 3500, + "product": "bht", + "details": { + "score": "6.5", + "some_option_name": "no" + } + } + ] + } + ] +}