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Add linter exceptions #1561

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2 changes: 2 additions & 0 deletions chemicaltoolbox/PaDEL/.lint_skip
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TestsCaseValidation
TestsParamInInputs
3 changes: 3 additions & 0 deletions chemicaltoolbox/autodock_vina/docking/.lint_skip
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ConditionalParamTypeBool
TestsCaseValidation
TestsExpectNumOutputs
1 change: 1 addition & 0 deletions chemicaltoolbox/autodock_vina/prepare_box/.lint_skip
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XMLOrder
1 change: 1 addition & 0 deletions chemicaltoolbox/autodock_vina/prepare_ligand/.lint_skip
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1 change: 1 addition & 0 deletions chemicaltoolbox/autodock_vina/prepare_receptor/.lint_skip
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3 changes: 3 additions & 0 deletions chemicaltoolbox/chembl/.lint_skip
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InputsNameRedundantArgument
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ValidDatatypes
1 change: 1 addition & 0 deletions chemicaltoolbox/chemfp/.lint_skip
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ValidDatatypes
1 change: 1 addition & 0 deletions chemicaltoolbox/confab/.lint_skip
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XMLOrder
1 change: 1 addition & 0 deletions chemicaltoolbox/data_source/get_online_data/.lint_skip
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CitationsNoValid
3 changes: 3 additions & 0 deletions chemicaltoolbox/data_source/get_pubchem/.lint_skip
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CitationsMissing
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3 changes: 3 additions & 0 deletions chemicaltoolbox/fpocket/.lint_skip
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TestsCaseValidation
TestsExpectNumOutputs
TestsParamInInputs
3 changes: 3 additions & 0 deletions chemicaltoolbox/im-pipelines/.lint_skip
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ConditionalParamTypeBool
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TestsExpectNumOutputs
1 change: 1 addition & 0 deletions chemicaltoolbox/mordred/.lint_skip
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XMLOrder
3 changes: 3 additions & 0 deletions chemicaltoolbox/natural_product_likeness/.lint_skip
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InputsBoolDistinctValues
OutputsLabelDuplicatedFilter
TestsExpectNumOutputs
2 changes: 2 additions & 0 deletions chemicaltoolbox/openbabel/.lint_skip
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1 change: 1 addition & 0 deletions chemicaltoolbox/openduck/.lint_skip
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2 changes: 2 additions & 0 deletions chemicaltoolbox/rdkit/.lint_skip
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1 change: 1 addition & 0 deletions chemicaltoolbox/rdock/.lint_skip
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2 changes: 2 additions & 0 deletions chemicaltoolbox/rxdock/.lint_skip
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ToolVersionPEP404
1 change: 1 addition & 0 deletions chemicaltoolbox/silicos-it/align-it/.lint_skip
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ValidDatatypes
1 change: 1 addition & 0 deletions chemicaltoolbox/silicos-it/qed/.lint_skip
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3 changes: 3 additions & 0 deletions chemicaltoolbox/silicos-it/shape-it/.lint_skip
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OutputsLabelDuplicatedFilter
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1 change: 1 addition & 0 deletions chemicaltoolbox/simsearch/.lint_skip
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TestsCaseValidation
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InputsMissing
1 change: 1 addition & 0 deletions tools/GraphClust/AggregateAlignments/.lint_skip
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5 changes: 5 additions & 0 deletions tools/GraphClust/AlignCluster/.lint_skip
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InputsNameRedundantArgument
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XSD
3 changes: 3 additions & 0 deletions tools/GraphClust/CMFinder/.lint_skip
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TestsCaseValidation
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3 changes: 3 additions & 0 deletions tools/GraphClust/CollectResults/.lint_skip
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ConditionalParamTypeBool
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OutputsFormat
2 changes: 2 additions & 0 deletions tools/GraphClust/CollectResultsNoAlign/.lint_skip
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ConditionalParamTypeBool
OutputsFormat
3 changes: 3 additions & 0 deletions tools/GraphClust/GSPAN/.lint_skip
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OutputsFormat
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XSD
4 changes: 4 additions & 0 deletions tools/GraphClust/LocARNAGraphClust/.lint_skip
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InputsNameRedundantArgument
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4 changes: 4 additions & 0 deletions tools/GraphClust/NSPDK/.lint_skip
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ConditionalParamTypeBool
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2 changes: 2 additions & 0 deletions tools/GraphClust/Plotting/.lint_skip
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CitationsNoValid
HelpEmpty
1 change: 1 addition & 0 deletions tools/GraphClust/PrepareForMlocarna/.lint_skip
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CitationsNoValid
1 change: 1 addition & 0 deletions tools/GraphClust/Preprocessing/.lint_skip
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OutputsNameInvalidCheetah
5 changes: 5 additions & 0 deletions tools/GraphClust/Structure_GSPAN/.lint_skip
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InputsNameRedundantArgument
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1 change: 1 addition & 0 deletions tools/agat/.lint_skip
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2 changes: 2 additions & 0 deletions tools/antismash/.lint_skip
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XMLOrder
1 change: 1 addition & 0 deletions tools/atactk_trim_adapters/.lint_skip
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OutputsLabelDuplicatedNoFilter
3 changes: 3 additions & 0 deletions tools/bamhash/.lint_skip
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CitationsNoValid
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1 change: 1 addition & 0 deletions tools/barcode_collapse/.lint_skip
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OutputsLabelDuplicatedNoFilter
5 changes: 5 additions & 0 deletions tools/bismark/.lint_skip
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ConditionalParamTypeBool
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OutputsFilterExpression
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TestsExpectNumOutputs
2 changes: 2 additions & 0 deletions tools/blobtoolkit/.lint_skip
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OutputsFilterExpression
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1 change: 1 addition & 0 deletions tools/canu/.lint_skip
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XMLOrder
2 changes: 2 additions & 0 deletions tools/cellpose/.lint_skip
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TestsCaseValidation
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5 changes: 5 additions & 0 deletions tools/cellprofiler/.lint_skip
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InputsNameDuplicate
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InputsSelectOptionDuplicateValue
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2 changes: 2 additions & 0 deletions tools/chatgpt/.lint_skip
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1 change: 1 addition & 0 deletions tools/chipseeker/.lint_skip
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1 change: 1 addition & 0 deletions tools/circexplorer/.lint_skip
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1 change: 1 addition & 0 deletions tools/combine_metaphlan_humann/.lint_skip
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1 change: 1 addition & 0 deletions tools/compare_humann2_output/.lint_skip
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CitationsMissing
5 changes: 5 additions & 0 deletions tools/edta/.lint_skip
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InputsNameRedundantArgument
OutputsFilterExpression
OutputsLabelDuplicatedFilter
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TestsParamInInputs
2 changes: 2 additions & 0 deletions tools/epicseg/.lint_skip
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TestsCaseValidation
TestsOutputCheckDiscovered
3 changes: 3 additions & 0 deletions tools/file_manipulation/.lint_skip
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OutputsFormatInput
TestsCaseValidation
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2 changes: 2 additions & 0 deletions tools/find_subsequences/.lint_skip
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InputsSelectOptionDuplicateValue
TestsCaseValidation
1 change: 1 addition & 0 deletions tools/flexynesis/.lint_skip
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TestsCaseValidation
1 change: 1 addition & 0 deletions tools/flux/.lint_skip
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3 changes: 3 additions & 0 deletions tools/footprint/.lint_skip
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TestsCaseValidation
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XSD
3 changes: 3 additions & 0 deletions tools/format_cd_hit_output/.lint_skip
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CitationsNoValid
TestsCaseValidation
TestsExpectNumOutputs
2 changes: 2 additions & 0 deletions tools/format_metaphlan2_output/.lint_skip
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CitationsNoValid
XMLOrder
4 changes: 4 additions & 0 deletions tools/gotohscan/.lint_skip
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InputsNameRedundantArgument
OutputsLabelDuplicatedFilter
TestsExpectNumOutputs
TestsOutputName
5 changes: 5 additions & 0 deletions tools/hclust2/.lint_skip
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CitationsMissing
InputsSelectOptionDuplicateText
InputsSelectOptionDuplicateValue
OutputsLabelDuplicatedFilter
TestsCaseValidation
1 change: 1 addition & 0 deletions tools/hictk/.lint_skip
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ValidDatatypes
2 changes: 2 additions & 0 deletions tools/hicup/.lint_skip
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TestsCaseValidation
TestsExpectNumOutputs
1 change: 1 addition & 0 deletions tools/image_processing/bia-ftplinks/.lint_skip
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XSD
1 change: 1 addition & 0 deletions tools/image_processing/graphicsmagick/.lint_skip
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ValidDatatypes
1 change: 1 addition & 0 deletions tools/image_processing/imagej2/.lint_skip
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TestsCaseValidation
1 change: 1 addition & 0 deletions tools/instagraal/.lint_skip
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XMLOrder
1 change: 1 addition & 0 deletions tools/itsx/.lint_skip
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OutputsFilterExpression
3 changes: 3 additions & 0 deletions tools/jbrowse2/.lint_skip
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TestsCaseValidation
TestsParamInInputs
ValidDatatypes
1 change: 1 addition & 0 deletions tools/lighter/.lint_skip
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1 change: 1 addition & 0 deletions tools/mafft/.lint_skip
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1 change: 1 addition & 0 deletions tools/methyldackel/.lint_skip
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2 changes: 2 additions & 0 deletions tools/methylkit/.lint_skip
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TestsCaseValidation
TestsExpectNumOutputs
1 change: 1 addition & 0 deletions tools/mgnify_seqprep/.lint_skip
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TestsCaseValidation
2 changes: 2 additions & 0 deletions tools/minced/.lint_skip
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OutputsLabelDuplicatedFilter
TestsExpectNumOutputs
1 change: 1 addition & 0 deletions tools/minipolish/.lint_skip
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XMLOrder
2 changes: 2 additions & 0 deletions tools/mitohifi/.lint_skip
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OutputsFilterExpression
TestsCaseValidation
1 change: 1 addition & 0 deletions tools/motus/.lint_skip
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ValidDatatypes
2 changes: 2 additions & 0 deletions tools/music_deconvolution/.lint_skip
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TestsCaseValidation
TestsParamInInputs
2 changes: 2 additions & 0 deletions tools/nanopolish/.lint_skip
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1 change: 1 addition & 0 deletions tools/netboxr/.lint_skip
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TestsExpectNumOutputs
3 changes: 3 additions & 0 deletions tools/nextdenovo/.lint_skip
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OutputsLabelDuplicatedFilter
OutputsNameDuplicated
TestsCaseValidation
9 changes: 9 additions & 0 deletions tools/openms/.lint_skip
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DatatypesCustomConf
InputsSelectOptionalRadio
OutputsFormatInput
OutputsLabelDuplicatedNoFilter
RequirementVersionMissing
TestsMissing
ValidDatatypes
XMLOrder
XSD
3 changes: 3 additions & 0 deletions tools/pandas_rolling_window/.lint_skip
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CitationsMissing
ConditionalOptionMissing
ValidDatatypes
1 change: 1 addition & 0 deletions tools/pg_tools/.lint_skip
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CitationsNoValid
3 changes: 3 additions & 0 deletions tools/pharmcat/.lint_skip
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OutputsLabelDuplicatedFilter
TestsCaseValidation
TestsParamInInputs
3 changes: 3 additions & 0 deletions tools/piranha/.lint_skip
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ConditionalWhenMissing
TestsCaseValidation
TestsExpectNumOutputs
1 change: 1 addition & 0 deletions tools/plotly_parallel_coordinates_plot/.lint_skip
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TestsCaseValidation
1 change: 1 addition & 0 deletions tools/plotly_regression_performance_plots/.lint_skip
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CitationsMissing
5 changes: 5 additions & 0 deletions tools/protease_prediction/.lint_skip
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DatatypesCustomConf
OutputsLabelDuplicatedFilter
TestsCaseValidation
TestsExpectNumOutputs
XSD
1 change: 1 addition & 0 deletions tools/replaceColumn/.lint_skip
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CitationsMissing
2 changes: 2 additions & 0 deletions tools/rna_tools/antarna/.lint_skip
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CitationsNoValid
CommandInterpreterDeprecated
3 changes: 3 additions & 0 deletions tools/rna_tools/aresite2/.lint_skip
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TestsCaseValidation
TestsOutputDefined
TestsParamInInputs
3 changes: 3 additions & 0 deletions tools/rna_tools/blockclust/.lint_skip
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ConditionalWhenMissing
OutputsFilterExpression
TestsCaseValidation
1 change: 1 addition & 0 deletions tools/rna_tools/cmsearch_deoverlap/.lint_skip
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TestsCaseValidation
3 changes: 3 additions & 0 deletions tools/rna_tools/cmv/.lint_skip
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TestsExpectNumOutputs
ValidDatatypes
3 changes: 3 additions & 0 deletions tools/rna_tools/cofold/.lint_skip
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CommandInterpreterDeprecated
TestsCaseValidation
XMLOrder
2 changes: 2 additions & 0 deletions tools/rna_tools/dewseq/.lint_skip
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TestsCaseValidation
TestsExpectNumOutputs
4 changes: 4 additions & 0 deletions tools/rna_tools/exparna/.lint_skip
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ConditionalParamTypeBool
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TestsExpectNumOutputs
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1 change: 1 addition & 0 deletions tools/rna_tools/graphprot/.lint_skip
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2 changes: 2 additions & 0 deletions tools/rna_tools/htseq-clip/.lint_skip
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TestsExpectNumOutputs
4 changes: 4 additions & 0 deletions tools/rna_tools/infernal/.lint_skip
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DatatypesCustomConf
OutputsFilterExpression
TestsCaseValidation
ValidDatatypes
1 change: 1 addition & 0 deletions tools/rna_tools/intarna/.lint_skip
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OutputsFilterExpression
3 changes: 3 additions & 0 deletions tools/rna_tools/locarna/.lint_skip
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OutputsFilterExpression
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3 changes: 3 additions & 0 deletions tools/rna_tools/mea/.lint_skip
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ConditionalParamTypeBool
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TestsParamInInputs
2 changes: 2 additions & 0 deletions tools/rna_tools/miRDeep2/miRDeep2/.lint_skip
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TestsExpectNumOutputs
XMLOrder
3 changes: 3 additions & 0 deletions tools/rna_tools/miRDeep2/miRDeep2_mapper/.lint_skip
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OutputsFilterExpression
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1 change: 1 addition & 0 deletions tools/rna_tools/mqc/.lint_skip
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2 changes: 2 additions & 0 deletions tools/rna_tools/paralyzer/.lint_skip
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1 change: 1 addition & 0 deletions tools/rna_tools/pipmir/.lint_skip
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2 changes: 2 additions & 0 deletions tools/rna_tools/rbpbench/.lint_skip
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CitationsMissing
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6 changes: 6 additions & 0 deletions tools/rna_tools/rcas/.lint_skip
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ConditionalParamTypeBool
OutputsNameInvalidCheetah
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TestsExpectNumOutputs
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XSD
2 changes: 2 additions & 0 deletions tools/rna_tools/ribotaper/.lint_skip
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XSD
2 changes: 2 additions & 0 deletions tools/rna_tools/rna_shapes/.lint_skip
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4 changes: 4 additions & 0 deletions tools/rna_tools/rnacode/.lint_skip
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InputsNameRedundantArgument
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1 change: 1 addition & 0 deletions tools/rna_tools/rnaformer/.lint_skip
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2 changes: 2 additions & 0 deletions tools/rna_tools/rnalien/.lint_skip
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4 changes: 4 additions & 0 deletions tools/rna_tools/rnaz/.lint_skip
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InputsNameRedundantArgument
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2 changes: 2 additions & 0 deletions tools/rna_tools/sshmm/.lint_skip
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OutputsFilterExpression
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1 change: 1 addition & 0 deletions tools/rna_tools/targetfinder/.lint_skip
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InputsNameDuplicate
3 changes: 3 additions & 0 deletions tools/rna_tools/trna_prediction/.lint_skip
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OutputsLabelDuplicatedFilter
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9 changes: 9 additions & 0 deletions tools/rna_tools/vienna_rna/.lint_skip
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ConditionalWhenMissing
InputsNameDuplicate
InputsNameRedundantArgument
OutputsLabelDuplicatedFilter
OutputsLabelDuplicatedNoFilter
TestsCaseValidation
TestsExpectNumOutputs
TestsOutputDefined
ValidDatatypes
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