galaxyproject · bernt-matthias · Nov 25, 2024
diff --git a/data_managers/data_manager_dram_database_downloader/.lint_skip b/data_managers/data_manager_dram_database_downloader/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/data_managers/data_manager_fetch_genome_dbkeys_all_fasta/.lint_skip b/data_managers/data_manager_fetch_genome_dbkeys_all_fasta/.lint_skip
@@ -1 +1,2 @@
 CitationsMissing
+TestsCaseValidation
diff --git a/data_managers/data_manager_fetch_refseq/.lint_skip b/data_managers/data_manager_fetch_refseq/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/data_managers/data_manager_genomic_super_signature_ravmodels/.lint_skip b/data_managers/data_manager_genomic_super_signature_ravmodels/.lint_skip
@@ -1 +1,2 @@
 CitationsMissing
+TestsCaseValidation
diff --git a/data_managers/data_manager_interproscan/.lint_skip b/data_managers/data_manager_interproscan/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/data_managers/data_manager_malt_index_builder/.lint_skip b/data_managers/data_manager_malt_index_builder/.lint_skip
@@ -1 +1,2 @@
+TestsCaseValidation
 XMLOrder
diff --git a/data_managers/data_manager_mapseq/data_manager/.lint_skip b/data_managers/data_manager_mapseq/data_manager/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/data_managers/data_manager_mash_sketch_builder/.lint_skip b/data_managers/data_manager_mash_sketch_builder/.lint_skip
@@ -1 +1,2 @@
+TestsCaseValidation
 XMLOrder
diff --git a/data_managers/data_manager_pangolin_data/.lint_skip b/data_managers/data_manager_pangolin_data/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/data_managers/data_manager_pharokka_database_fetcher/.lint_skip b/data_managers/data_manager_pharokka_database_fetcher/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/data_managers/data_manager_primer_scheme_bedfiles/.lint_skip b/data_managers/data_manager_primer_scheme_bedfiles/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/data_managers/data_manager_selection_background/.lint_skip b/data_managers/data_manager_selection_background/.lint_skip
@@ -1,2 +1,3 @@
 CitationsMissing
 HelpEmpty
+TestsCaseValidation
diff --git a/data_managers/data_manager_snpsift_dbnsfp/.lint_skip b/data_managers/data_manager_snpsift_dbnsfp/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/bamtools/bamtools/.lint_skip b/tool_collections/bamtools/bamtools/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/bamtools/bamtools_filter/.lint_skip b/tool_collections/bamtools/bamtools_filter/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/biotradis/.lint_skip b/tool_collections/biotradis/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/cufflinks/cuffcompare/.lint_skip b/tool_collections/cufflinks/cuffcompare/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/cufflinks/cuffdiff/.lint_skip b/tool_collections/cufflinks/cuffdiff/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/cufflinks/cufflinks/.lint_skip b/tool_collections/cufflinks/cufflinks/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/cufflinks/cuffmerge/.lint_skip b/tool_collections/cufflinks/cuffmerge/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/cufflinks/cuffquant/.lint_skip b/tool_collections/cufflinks/cuffquant/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/.lint_skip b/tool_collections/fastx_toolkit/fastq_quality_converter/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/.lint_skip b/tool_collections/fastx_toolkit/fastq_to_fasta/.lint_skip
@@ -0,0 +1,2 @@
+OutputsFilterExpression
+TestsCaseValidation
diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/.lint_skip b/tool_collections/fastx_toolkit/fastx_barcode_splitter/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/fastx_toolkit/fastx_clipper/.lint_skip b/tool_collections/fastx_toolkit/fastx_clipper/.lint_skip
@@ -1 +1,2 @@
 InputsSelectOptionsDeprecatedAttr
+TestsCaseValidation
diff --git a/tool_collections/galaxy_sequence_utils/fastq_filter/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_filter/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/galaxy_sequence_utils/fastq_groomer/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_groomer/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/galaxy_sequence_utils/fastq_manipulation/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_manipulation/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer/.lint_skip
@@ -1,2 +1,3 @@
 # Allow duplicated labels (since filters are disjoint)
-OutputsLabelDuplicatedFilter
+OutputsLabelDuplicatedFilterTestsCaseValidation
+TestsCaseValidation
diff --git a/tool_collections/galaxy_sequence_utils/fastq_trimmer/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_trimmer/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/kraken/.lint_skip b/tool_collections/kraken/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/kraken2/kraken2/.lint_skip b/tool_collections/kraken2/kraken2/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/samtools/.lint_skip b/tool_collections/samtools/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/samtools/bam_to_cram/.lint_skip b/tool_collections/samtools/bam_to_cram/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/samtools/cram_to_bam/.lint_skip b/tool_collections/samtools/cram_to_bam/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/samtools/sam_to_bam/.lint_skip b/tool_collections/samtools/sam_to_bam/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/samtools/samtools_ampliconclip/.lint_skip b/tool_collections/samtools/samtools_ampliconclip/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/samtools/samtools_bedcov/.lint_skip b/tool_collections/samtools/samtools_bedcov/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/samtools/samtools_calmd/.lint_skip b/tool_collections/samtools/samtools_calmd/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/samtools/samtools_coverage/.lint_skip b/tool_collections/samtools/samtools_coverage/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/samtools/samtools_depth/.lint_skip b/tool_collections/samtools/samtools_depth/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/samtools/samtools_fastx/.lint_skip b/tool_collections/samtools/samtools_fastx/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/samtools/samtools_fixmate/.lint_skip b/tool_collections/samtools/samtools_fixmate/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/samtools/samtools_markdup/.lint_skip b/tool_collections/samtools/samtools_markdup/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/samtools/samtools_merge/.lint_skip b/tool_collections/samtools/samtools_merge/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/samtools/samtools_mpileup/.lint_skip b/tool_collections/samtools/samtools_mpileup/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/samtools/samtools_slice_bam/.lint_skip b/tool_collections/samtools/samtools_slice_bam/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/samtools/samtools_stats/.lint_skip b/tool_collections/samtools/samtools_stats/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/snpsift/snpsift/.lint_skip b/tool_collections/snpsift/snpsift/.lint_skip
@@ -1,2 +1,3 @@
+TestsCaseValidation
 TestsMissing
 XMLOrder
diff --git a/tool_collections/vcflib/vcfbedintersect/.lint_skip b/tool_collections/vcflib/vcfbedintersect/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/vcflib/vcfcheck/.lint_skip b/tool_collections/vcflib/vcfcheck/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/vcflib/vcfgeno2haplo/.lint_skip b/tool_collections/vcflib/vcfgeno2haplo/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/vcflib/vcfleftalign/.lint_skip b/tool_collections/vcflib/vcfleftalign/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/vcflib/vcfprimers/.lint_skip b/tool_collections/vcflib/vcfprimers/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/vcflib/vcfrandomsample/.lint_skip b/tool_collections/vcflib/vcfrandomsample/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tool_collections/vcflib/vcfvcfintersect/.lint_skip b/tool_collections/vcflib/vcfvcfintersect/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/abricate/.lint_skip b/tools/abricate/.lint_skip
@@ -1 +1,2 @@
 InputsMissing
+TestsCaseValidation
diff --git a/tools/adapter_removal/.lint_skip b/tools/adapter_removal/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/add_input_name_as_column/.lint_skip b/tools/add_input_name_as_column/.lint_skip
@@ -1 +1,2 @@
 CitationsMissing
+TestsCaseValidation
diff --git a/tools/aegean/.lint_skip b/tools/aegean/.lint_skip
@@ -0,0 +1,2 @@
+TestsCaseValidation
+TestsParamInInputs
diff --git a/tools/aldex2/.lint_skip b/tools/aldex2/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/allegro/.lint_skip b/tools/allegro/.lint_skip
@@ -1 +1,2 @@
+TestsCaseValidation
 XMLOrder
diff --git a/tools/amplican/.lint_skip b/tools/amplican/.lint_skip
@@ -0,0 +1,2 @@
+TestsCaseValidation
+TestsParamInInputs
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/amrfinderplus/.lint_skip b/tools/amrfinderplus/.lint_skip
@@ -0,0 +1,6 @@
+OutputsFilterExpression): Filter ' input_option['input_mode']['input_select'] in ['nucleotide', 'nucl_prot'] and  input_option['input_mode']['nucleotide_flank5_size'] != 0 ' is no valid expression: unexpected indent (<unknown>, line 1
+OutputsFilterExpression): Filter ' input_option['input_mode']['input_select'] in ['nucleotide', 'nucl_prot'] ' is no valid expression: unexpected indent (<unknown>, line 1
+OutputsFilterExpression): Filter ' input_option['input_mode']['input_select'] in ['protein', 'nucl_prot']' is no valid expression: unexpected indent (<unknown>, line 1
+OutputsFilterExpression): Filter ' organism_options['organism_conditionnal']['organism_select'] == "add_organism" and organism_options['organism_conditionnal']['mutation_all'] is True  ' is no valid expression: unexpected indent (<unknown>, line 1
+TestsCaseValidation
+TestsParamInInputs
diff --git a/tools/anndata/.lint_skip b/tools/anndata/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/arriba/.lint_skip b/tools/arriba/.lint_skip
@@ -0,0 +1,3 @@
+OutputsFilterExpression): Filter ' output_fusions_discarded == True' is no valid expression: unexpected indent (<unknown>, line 1
+OutputsFilterExpression): Filter ' output_fusions_vcf == True' is no valid expression: unexpected indent (<unknown>, line 1
+TestsCaseValidation
@@ -1,4 +1,5 @@
 ConditionalParamTypeBool
 OutputsLabelDuplicatedFilter
+TestsCaseValidation
 TestsExpectNumOutputs
 XMLOrder
diff --git a/tools/artic/.lint_skip b/tools/artic/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/augustus/.lint_skip b/tools/augustus/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/b2btools/.lint_skip b/tools/b2btools/.lint_skip
@@ -1 +1,2 @@
 InputsNameRedundantArgument
+TestsCaseValidation
diff --git a/tools/bamutil/.lint_skip b/tools/bamutil/.lint_skip
@@ -1 +1 @@
-OutputsLabelDuplicatedFilter
+OutputsLabelDuplicatedFilterTestsCaseValidation
diff --git a/tools/bandage/.lint_skip b/tools/bandage/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/barcode_splitter/.lint_skip b/tools/barcode_splitter/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/basil/.lint_skip b/tools/basil/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/bayescan/.lint_skip b/tools/bayescan/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/bbtools/.lint_skip b/tools/bbtools/.lint_skip
@@ -0,0 +1,2 @@
+OutputsFilterExpression): Filter 'None' is no valid expression: compile(
+TestsCaseValidation
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/beacon2-import/.lint_skip b/tools/beacon2-import/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/beagle/.lint_skip b/tools/beagle/.lint_skip
@@ -1 +1,2 @@
+TestsParamInInputs
 ToolVersionPEP404
diff --git a/tools/bedtools/.lint_skip b/tools/bedtools/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/bigscape/.lint_skip b/tools/bigscape/.lint_skip
@@ -0,0 +1 @@
+OutputsFilterExpression): Filter ' clans_off == False ' is no valid expression: unexpected indent (<unknown>, line 1
diff --git a/tools/bigwig_outlier_bed/.lint_skip b/tools/bigwig_outlier_bed/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/bioext/.lint_skip b/tools/bioext/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/bioinformatics_cafe/.lint_skip b/tools/bioinformatics_cafe/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/biom_format/.lint_skip b/tools/biom_format/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/blast/.lint_skip b/tools/blast/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/bowtie2/.lint_skip b/tools/bowtie2/.lint_skip
@@ -1 +1,3 @@
 ConditionalParamTypeBool
+OutputsFilterExpression): Filter 'None' is no valid expression: compile(
+TestsCaseValidation
diff --git a/tools/bracken/.lint_skip b/tools/bracken/.lint_skip
@@ -0,0 +1 @@
+OutputsFilterExpression): Filter ' logfile_output == True ' is no valid expression: unexpected indent (<unknown>, line 1
diff --git a/tools/breseq/.lint_skip b/tools/breseq/.lint_skip
@@ -1,3 +1,4 @@
 InputsNameRedundantArgument
+TestsCaseValidation
 TestsExpectNumOutputs
 XMLOrder
diff --git a/tools/bwa/.lint_skip b/tools/bwa/.lint_skip
@@ -1 +1,3 @@
 ConditionalParamTypeBool
+OutputsFilterExpression): Filter 'None' is no valid expression: compile(
+TestsCaseValidation
diff --git a/tools/bwa_mem2/.lint_skip b/tools/bwa_mem2/.lint_skip
@@ -1,2 +1,4 @@
 ConditionalParamTypeBool
+OutputsFilterExpression): Filter 'None' is no valid expression: compile(
+TestsCaseValidation
 XMLOrder
diff --git a/tools/bwameth/.lint_skip b/tools/bwameth/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/checkm/.lint_skip b/tools/checkm/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/chewbbaca/.lint_skip b/tools/chewbbaca/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/chira/.lint_skip b/tools/chira/.lint_skip
@@ -1 +1,2 @@
 CitationsNoValid
+TestsCaseValidation
diff --git a/tools/chromeister/.lint_skip b/tools/chromeister/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
@@ -1 +1,2 @@
+TestsCaseValidation
 TestsExpectNumOutputs
diff --git a/tools/clustalw/.lint_skip b/tools/clustalw/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/cnvkit/.lint_skip b/tools/cnvkit/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/codeml/.lint_skip b/tools/codeml/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/cojac/.lint_skip b/tools/cojac/.lint_skip
@@ -0,0 +1,2 @@
+TestsCaseValidation
+TestsParamInInputs
diff --git a/tools/colabfold/.lint_skip b/tools/colabfold/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/collection_column_join/.lint_skip b/tools/collection_column_join/.lint_skip
@@ -1,3 +1,4 @@
 CitationsNoValid
 OutputsLabelDuplicatedFilter
+TestsCaseValidation
 TestsExpectNumOutputs
@@ -1 +1,2 @@
 CitationsNoValid
+TestsCaseValidation
diff --git a/tools/column_remove_by_header/.lint_skip b/tools/column_remove_by_header/.lint_skip
@@ -1 +1,2 @@
 CitationsNoValid
+TestsCaseValidation
diff --git a/tools/concoct/.lint_skip b/tools/concoct/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/cosg/.lint_skip b/tools/cosg/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/coverm/.lint_skip b/tools/coverm/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/crispr_studio/.lint_skip b/tools/crispr_studio/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/crossmap/.lint_skip b/tools/crossmap/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/cutadapt/.lint_skip b/tools/cutadapt/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/cwpair2/.lint_skip b/tools/cwpair2/.lint_skip
@@ -1 +1,2 @@
+TestsCaseValidation
 TestsExpectNumOutputs
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/deepmicro/.lint_skip b/tools/deepmicro/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/delly/.lint_skip b/tools/delly/.lint_skip
@@ -0,0 +1,2 @@
+TestsCaseValidation
+TestsParamInInputs
diff --git a/tools/deseq2/.lint_skip b/tools/deseq2/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/dexseq/.lint_skip b/tools/dexseq/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/diamond/.lint_skip b/tools/diamond/.lint_skip
@@ -1,2 +1,3 @@
 InputsNameRedundantArgument
 OutputsLabelDuplicatedFilter
+TestsCaseValidation
diff --git a/tools/diffbind/.lint_skip b/tools/diffbind/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/dimet/.lint_skip b/tools/dimet/.lint_skip
@@ -0,0 +1,2 @@
+TestsCaseValidation
+TestsParamInInputs
diff --git a/tools/disco/.lint_skip b/tools/disco/.lint_skip
@@ -1,4 +1,5 @@
 CitationsNoValid
 InputsNameDuplicateOutput
+TestsCaseValidation
 TestsExpectNumOutputs
 XMLOrder
diff --git a/tools/dram/.lint_skip b/tools/dram/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/drep/.lint_skip b/tools/drep/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/dropletutils/.lint_skip b/tools/dropletutils/.lint_skip
@@ -0,0 +1,2 @@
+TestsCaseValidation
+TestsParamInInputs
diff --git a/tools/edger/.lint_skip b/tools/edger/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/egsea/.lint_skip b/tools/egsea/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
@@ -1,5 +1,6 @@
 InputsSelectOptionDuplicateText
 OutputsLabelDuplicatedNoFilter
+TestsCaseValidation
 TestsMissing
 TestsParamInInputs
 ToolIDWhitespace

diff --git a/tools/ena_upload/.lint_skip b/tools/ena_upload/.lint_skip
@@ -0,0 +1,2 @@
+OutputsFilterExpression): Filter ' action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables" or action_options['input_format_conditional']['input_format'] == "isa_json"' is no valid expression: unexpected indent (<unknown>, line 1
+TestsCaseValidation
diff --git a/tools/ensembl_vep/.lint_skip b/tools/ensembl_vep/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/episcanpy/.lint_skip b/tools/episcanpy/.lint_skip
@@ -0,0 +1,2 @@
+TestsCaseValidation
+TestsParamInInputs
diff --git a/tools/evidencemodeler/.lint_skip b/tools/evidencemodeler/.lint_skip
@@ -0,0 +1,2 @@
+TestsCaseValidation
+TestsParamInInputs
diff --git a/tools/export2graphlan/.lint_skip b/tools/export2graphlan/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/extract_genomic_dna/.lint_skip b/tools/extract_genomic_dna/.lint_skip
@@ -1 +1,2 @@
+TestsCaseValidation
 ToolIDWhitespace
diff --git a/tools/falco/.lint_skip b/tools/falco/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/fargene/.lint_skip b/tools/fargene/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/fasta_nucleotide_color_plot/.lint_skip b/tools/fasta_nucleotide_color_plot/.lint_skip
@@ -1 +1,2 @@
+TestsCaseValidation
 XMLOrder
diff --git a/tools/fastk/.lint_skip b/tools/fastk/.lint_skip
@@ -0,0 +1 @@
+OutputsFilterExpression): Filter ' sorted_table['sorted_table_option'] != 'no' ' is no valid expression: unexpected indent (<unknown>, line 1
diff --git a/tools/fastp/.lint_skip b/tools/fastp/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/fastq_dl/.lint_skip b/tools/fastq_dl/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/fastqc/.lint_skip b/tools/fastqc/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/fasttree/.lint_skip b/tools/fasttree/.lint_skip
@@ -1,2 +1,3 @@
-# the bool is used in a filter and an if statement of the command block which works
 InputsBoolDistinctValues
+TestsCaseValidation
+# the bool is used in a filter and an if statement of the command block which works
diff --git a/tools/featurecounts/.lint_skip b/tools/featurecounts/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/fermikit/.lint_skip b/tools/fermikit/.lint_skip
@@ -1 +1,2 @@
+TestsCaseValidation
 ToolVersionPEP404
diff --git a/tools/filtlong/.lint_skip b/tools/filtlong/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/flair/.lint_skip b/tools/flair/.lint_skip
@@ -1 +1,2 @@
 InputsNameRedundantArgument
+TestsCaseValidation
diff --git a/tools/flash/.lint_skip b/tools/flash/.lint_skip
@@ -1,4 +1,5 @@
 InputsBoolDistinctValues
 InputsNameRedundantArgument
 OutputsLabelDuplicatedFilter
+TestsCaseValidation
 XMLOrder
diff --git a/tools/freebayes/.lint_skip b/tools/freebayes/.lint_skip
@@ -1,3 +1,4 @@
 InputsNameRedundantArgument
+TestsCaseValidation
 TestsExpectNumOutputs
 XMLOrder
diff --git a/tools/freec/.lint_skip b/tools/freec/.lint_skip
@@ -0,0 +1 @@
+TestsCaseValidation
diff --git a/tools/freyja/.lint_skip b/tools/freyja/.lint_skip
@@ -0,0 +1,2 @@
+OutputsFilterExpression
+TestsCaseValidation
diff --git a/tools/funannotate/.lint_skip b/tools/funannotate/.lint_skip
@@ -0,0 +1 @@
+BioToolsValid
diff --git a/tools/gatk4/.lint_skip b/tools/gatk4/.lint_skip
@@ -1,5 +1,6 @@
 InputsNameDuplicate
 InputsNameRedundantArgument
+TestsCaseValidation
 TestsExpectNumOutputs
 TestsParamInInputs
 ToolVersionPEP404
Original file line number	Diff line number	Diff line change
		@@ -1 +1,2 @@
		InputsSelectOptionsDeprecatedAttr
		TestsCaseValidation
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		OutputsLabelDuplicatedFilter
		OutputsLabelDuplicatedFilterTestsCaseValidation
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		OutputsFilterExpression): Filter 'None' is no valid expression: compile(
		TestsCaseValidation
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		OutputsFilterExpression): Filter ' clans_off == False ' is no valid expression: unexpected indent (<unknown>, line 1
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		OutputsFilterExpression): Filter ' logfile_output == True ' is no valid expression: unexpected indent (<unknown>, line 1
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		OutputsFilterExpression): Filter ' action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables" or action_options['input_format_conditional']['input_format'] == "isa_json"' is no valid expression: unexpected indent (<unknown>, line 1
		TestsCaseValidation
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		OutputsFilterExpression): Filter ' sorted_table['sorted_table_option'] != 'no' ' is no valid expression: unexpected indent (<unknown>, line 1