Add linter exceptions for 24.2 #1584
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| InputsNameRedundantArgument | ||
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| ConditionalParamTypeBool | ||
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| InputsBoolDistinctValues | ||
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| InputsNameRedundantArgument | ||
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| TestsExpectNumOutputs | ||
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| chemicaltoolbox/PaDEL | ||
| chemicaltoolbox/autodock_vina/docking | ||
| chemicaltoolbox/autodock_vina/prepare_box | ||
| chemicaltoolbox/autodock_vina/prepare_ligand | ||
| chemicaltoolbox/autodock_vina/prepare_receptor | ||
| chemicaltoolbox/chembl | ||
| chemicaltoolbox/chemfp | ||
| chemicaltoolbox/confab | ||
| chemicaltoolbox/data_source/get_online_data | ||
| chemicaltoolbox/data_source/get_pdb | ||
| chemicaltoolbox/data_source/get_pubchem | ||
| chemicaltoolbox/fpocket | ||
| chemicaltoolbox/im-pipelines | ||
| chemicaltoolbox/mordred | ||
| chemicaltoolbox/natural_product_likeness | ||
| chemicaltoolbox/openbabel | ||
| chemicaltoolbox/openduck | ||
| chemicaltoolbox/openmg | ||
| chemicaltoolbox/osra | ||
| chemicaltoolbox/rdkit | ||
| chemicaltoolbox/rdock | ||
| chemicaltoolbox/rxdock | ||
| chemicaltoolbox/silicos-it/align-it | ||
| chemicaltoolbox/silicos-it/qed | ||
| chemicaltoolbox/silicos-it/shape-it | ||
| chemicaltoolbox/silicos-it/strip-it | ||
| chemicaltoolbox/simsearch | ||
| chemicaltoolbox/spectral_hk | ||
| chemicaltoolbox/sucos | ||
| chemicaltoolbox/sygma | ||
| chemicaltoolbox/xchem-deep | ||
| data_managers/data_manager_motus_db_downloader | ||
| data_managers/data_manager_sortmerna_database_downloader | ||
| deprecated/tools/augustus | ||
| packages/package_pkiss_2_2_12 | ||
| packages/package_quast_3_1 | ||
| packages/package_rnashapes_3_2_5 | ||
| tools/10x_bamtofastq | ||
| tools/GraphClust/AggregateAlignments | ||
| tools/GraphClust/AlignCluster | ||
| tools/GraphClust/CMFinder | ||
| tools/GraphClust/CollectResults | ||
| tools/GraphClust/CollectResultsNoAlign | ||
| tools/GraphClust/GSPAN | ||
| tools/GraphClust/LocARNAGraphClust | ||
| tools/GraphClust/NSPDK | ||
| tools/GraphClust/Plotting | ||
| tools/GraphClust/PrepareForMlocarna | ||
| tools/GraphClust/Preprocessing | ||
| tools/GraphClust/Structure_GSPAN | ||
| tools/agat | ||
| tools/antismash | ||
| tools/atactk_trim_adapters | ||
| tools/bamhash | ||
| tools/barcode_collapse | ||
| tools/bigwig_to_bedgraph | ||
| tools/bioimaging | ||
| tools/biomodelsML | ||
| tools/bionano | ||
| tools/bismark | ||
| tools/blobtoolkit | ||
| tools/blockbuster | ||
| tools/canu | ||
| tools/cellpose | ||
| tools/cellprofiler | ||
| tools/cellprofiler_v4 | ||
| tools/chatgpt | ||
| tools/chipseeker | ||
| tools/circexplorer | ||
| tools/combine_metaphlan_humann | ||
| tools/compare_humann2_output | ||
| tools/cpat | ||
| tools/crt | ||
| tools/diff | ||
| tools/diffbind | ||
| tools/ear | ||
| tools/edta | ||
| tools/epicseg | ||
| tools/fastq_info | ||
| tools/file_manipulation | ||
| tools/find_subsequences | ||
| tools/flexynesis | ||
| tools/flux | ||
| tools/flye | ||
| tools/footprint | ||
| tools/format_cd_hit_output | ||
| tools/format_metaphlan2_output | ||
| tools/gfastats | ||
| tools/glimmer_hmm | ||
| tools/gotohscan | ||
| tools/graph_converter | ||
| tools/graphclust | ||
| tools/graphmap | ||
| tools/hclust2 | ||
| tools/hictk | ||
| tools/hicup | ||
| tools/homer | ||
| tools/illumina_methylation_analyser | ||
| tools/image_processing/bia-ftplinks | ||
| tools/image_processing/graphicsmagick | ||
| tools/image_processing/imagej2 | ||
| tools/image_processing/woundhealing | ||
| tools/instagraal | ||
| tools/iprscan5 | ||
| tools/itsx | ||
| tools/jbrowse2 | ||
| tools/jupyter_job | ||
| tools/labels | ||
| tools/lighter | ||
| tools/mafft | ||
| tools/mave_tools/mavedb | ||
| tools/methtools | ||
| tools/methyldackel | ||
| tools/methylkit | ||
| tools/metilene | ||
| tools/mgnify_seqprep | ||
| tools/miclip | ||
| tools/minced | ||
| tools/minipolish | ||
| tools/mitohifi | ||
| tools/molecule2gspan | ||
| tools/motus | ||
| tools/music_deconvolution | ||
| tools/nanopolish | ||
| tools/netboxr | ||
| tools/nextdenovo | ||
| tools/nucleosome_prediction | ||
| tools/numeric_clustering | ||
| tools/openms | ||
| tools/pandas_rolling_window | ||
| tools/peakachu | ||
| tools/perf | ||
| tools/pfamscan | ||
| tools/pg_tools | ||
| tools/pharmcat | ||
| tools/piranha | ||
| tools/platypus | ||
| tools/plotly_ml_performance_plots | ||
| tools/plotly_parallel_coordinates_plot | ||
| tools/plotly_regression_performance_plots | ||
| tools/protease_prediction | ||
| tools/protein_properties | ||
| tools/proteomics/improviser | ||
| tools/racon | ||
| tools/repeat_masker | ||
| tools/replaceColumn | ||
| tools/rest_tool | ||
| tools/rna_tools/antarna | ||
| tools/rna_tools/aresite2 | ||
| tools/rna_tools/blockclust | ||
| tools/rna_tools/cmsearch_deoverlap | ||
| tools/rna_tools/cmv | ||
| tools/rna_tools/cofold | ||
| tools/rna_tools/compalignp | ||
| tools/rna_tools/coprarna | ||
| tools/rna_tools/dewseq | ||
| tools/rna_tools/dorina | ||
| tools/rna_tools/dot2ct | ||
| tools/rna_tools/dotknot | ||
| tools/rna_tools/exparna | ||
| tools/rna_tools/graphprot | ||
| tools/rna_tools/htseq-clip | ||
| tools/rna_tools/infernal | ||
| tools/rna_tools/inforna | ||
| tools/rna_tools/intarna | ||
| tools/rna_tools/kinwalker | ||
| tools/rna_tools/locarna | ||
| tools/rna_tools/mea | ||
| tools/rna_tools/miRDeep2/miRDeep2 | ||
| tools/rna_tools/miRDeep2/miRDeep2_mapper | ||
| tools/rna_tools/miRDeep2/miRDeep2_quantifier | ||
| tools/rna_tools/mqc | ||
| tools/rna_tools/nastiseq | ||
| tools/rna_tools/paralyzer | ||
| tools/rna_tools/pipmir | ||
| tools/rna_tools/rRNA | ||
| tools/rna_tools/rbpbench | ||
| tools/rna_tools/rcas | ||
| tools/rna_tools/reago | ||
| tools/rna_tools/remurna | ||
| tools/rna_tools/ribotaper | ||
| tools/rna_tools/rna_shapes | ||
| tools/rna_tools/rnabob | ||
| tools/rna_tools/rnacode | ||
| tools/rna_tools/rnacommender | ||
| tools/rna_tools/rnaformer | ||
| tools/rna_tools/rnalien | ||
| tools/rna_tools/rnasnp | ||
| tools/rna_tools/rnaz | ||
| tools/rna_tools/selectsequencesfrommsa | ||
| tools/rna_tools/sortmerna | ||
| tools/rna_tools/sshmm | ||
| tools/rna_tools/targetfinder | ||
| tools/rna_tools/trna_prediction | ||
| tools/rna_tools/vienna_rna | ||
| tools/sailfish | ||
| tools/salmon | ||
| tools/sambamba | ||
| tools/sed | ||
| tools/segemehl | ||
| tools/sklearn | ||
| tools/splitfasta | ||
| tools/statistics | ||
| tools/stress_ng | ||
| tools/tabpfn | ||
| tools/tapscan | ||
| tools/text_processing/add_line_to_file | ||
| tools/text_processing/column_arrange_by_header | ||
| tools/text_processing/join_files_on_column_fuzzy | ||
| tools/text_processing/split_file_on_column | ||
| tools/text_processing/split_file_to_collection | ||
| tools/text_processing/text_processing | ||
| tools/tgsgapcloser | ||
| tools/tiara | ||
| tools/tool_recommendation_model | ||
| tools/trim_galore | ||
| tools/uniprot_rest_interface | ||
| tools/vt | ||
| tools/whisper | ||
| tools/wordcloud | ||
| tools/wtdbg |
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| Linting tool /home/nilchia/Documents/github/bgruening/galaxytools/tools/wtdbg/wtdbg.xml | ||
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| .. WARNING (TestsCaseValidation): Test 3: failed to validate test parameters against inputs - tests won't run on a modern Galaxy tool profile version. Validation errors are [Invalid parameter name found asm|l] | ||
| .. CHECK (TestsNoValid): 3 test(s) found. | ||
| .. ERROR (TestsParamInInputs): Test 3: Test param l not found in the inputs | ||
| .. ERROR (TestsParamInInputs): Test 3: Test param m not found in the inputs | ||
| .. INFO (OutputsNumber): 1 outputs found. | ||
| .. INFO (InputsNum): Found 29 input parameters. | ||
| .. CHECK (HelpPresent): Tool contains help section. | ||
| .. CHECK (HelpValidRST): Help contains valid reStructuredText. | ||
| .. CHECK (ToolIDValid): Tool defines an id [wtdbg]. | ||
| .. CHECK (ToolNameValid): Tool defines a name [WTDBG2]. | ||
| .. CHECK (ToolProfileValid): Tool specifies profile version [20.01]. | ||
| .. CHECK (ToolVersionValid): Tool defines a version [2.5+galaxy0]. | ||
| .. INFO (CommandInfo): Tool contains a command. | ||
| .. CHECK (CitationsFound): Found 1 citations. | ||
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| InputsNameRedundantArgument | ||
| ToolNameWhitespace | ||
| XMLOrder | ||
| XSD | ||
| TestsCaseValidation |
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| TestsParamInInputs | ||
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| TestsCaseValidation |
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| ConditionalParamTypeBool | ||
| InputsNameRedundantArgument | ||
| OutputsFormat |
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| ConditionalParamTypeBool | ||
| OutputsFormat |
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| OutputsFormat | ||
| XSD | ||
| TestsCaseValidation |
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| InputsNameRedundantArgument | ||
| TestsCaseValidation | ||
| ValidDatatypes | ||
| XSD |
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| ConditionalParamTypeBool | ||
| TestsExpectNumOutputs | ||
| TestsCaseValidation |
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| CitationsNoValid | ||
| HelpEmpty |
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| OutputsNameInvalidCheetah |
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| InputsNameRedundantArgument | ||
| OutputsFormat | ||
| TestsParamInInputs | ||
| XSD | ||
| TestsCaseValidation |
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| TestsCaseValidation |
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| XMLOrder | ||
| TestsCaseValidation |
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| TestsCaseValidation |
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| ConditionalParamTypeBool | ||
| InputsNameRedundantArgument | ||
| TestsExpectNumOutputs | ||
| TestsCaseValidation |
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| TestsCaseValidation |
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| XMLOrder |
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| TestsCaseValidation | ||
| ValidDatatypes |
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| InputsNameDuplicate | ||
| InputsSelectOptionDuplicateText | ||
| InputsSelectOptionDuplicateValue | ||
| TestsParamInInputs | ||
| TestsCaseValidation |
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| TestsCaseValidation | ||
| ValidDatatypes |
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| TestsCaseValidation |
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| TestsCaseValidation |
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| XMLOrder |
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| CitationsMissing |
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| InputsNameRedundantArgument | ||
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| TestsParamInInputs |
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can this be removed