diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index f2ecdfe79a3..95a09fa0a8c 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -75,7 +75,7 @@ jobs:
         echo 'Using ${{ steps.discover.outputs.chunk-count }} chunks (${{ steps.discover.outputs.chunk-list }})'
 
   lint:
-    name: Check for missing containers
+    name: Lint tool-list
     needs: setup
     if: ${{ needs.setup.outputs.repository-list != '' || needs.setup.outputs.tool-list != '' }}
     runs-on: ubuntu-latest
@@ -101,9 +101,10 @@ jobs:
       id: lint
       with:
         mode: lint
+        fail-level: warn
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
-        additional-planemo-options: --biocontainers -s stdio,tests,output,inputs,help,general,command,citations,tool_xsd,xml_order,tool_urls,shed_metadata,urls,readme,shed_yaml,repository_dependencies,tool_dependencies_actions,tool_dependencies_sha256sum,tool_dependencies_xsd,expansion
+        additional-planemo-options: --biocontainers
     - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index eccab2f5c9b..87249ab8fcf 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -123,21 +123,12 @@ jobs:
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
-
-    - name: Set fail level for pull request
-      if: ${{ github.event_name == 'pull_request' }}
-      run:
-        echo "FAIL_LEVEL=warn" >> "$GITHUB_ENV"
-    - name: Set fail level for merge
-      if: ${{ github.event_name != 'pull_request' }}
-      run:
-        echo "FAIL_LEVEL=error" >> "$GITHUB_ENV"
     - name: Planemo lint
       uses: galaxyproject/planemo-ci-action@v1
       id: lint
       with:
         mode: lint
-        fail-level: ${{ env.FAIL_LEVEL }}
+        fail-level: warn
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
     - uses: actions/upload-artifact@v4
diff --git a/data_managers/data_manager_bowtie2_index_builder/.lint_skip b/data_managers/data_manager_bowtie2_index_builder/.lint_skip
new file mode 100644
index 00000000000..855dee9e6e0
--- /dev/null
+++ b/data_managers/data_manager_bowtie2_index_builder/.lint_skip
@@ -0,0 +1,2 @@
+CitationsMissing
+XMLOrder
diff --git a/data_managers/data_manager_bowtie_index_builder/.lint_skip b/data_managers/data_manager_bowtie_index_builder/.lint_skip
new file mode 100644
index 00000000000..fd9005475bf
--- /dev/null
+++ b/data_managers/data_manager_bowtie_index_builder/.lint_skip
@@ -0,0 +1 @@
+TestsMissing
diff --git a/data_managers/data_manager_build_kma_index/.lint_skip b/data_managers/data_manager_build_kma_index/.lint_skip
new file mode 100644
index 00000000000..7d044e96aea
--- /dev/null
+++ b/data_managers/data_manager_build_kma_index/.lint_skip
@@ -0,0 +1 @@
+HelpEmpty
diff --git a/data_managers/data_manager_build_kraken_database/.lint_skip b/data_managers/data_manager_build_kraken_database/.lint_skip
new file mode 100644
index 00000000000..b394139e289
--- /dev/null
+++ b/data_managers/data_manager_build_kraken_database/.lint_skip
@@ -0,0 +1,2 @@
+HelpEmpty
+TestsMissing
diff --git a/data_managers/data_manager_bwa_mem_index_builder/.lint_skip b/data_managers/data_manager_bwa_mem_index_builder/.lint_skip
new file mode 100644
index 00000000000..46f5e08e85b
--- /dev/null
+++ b/data_managers/data_manager_bwa_mem_index_builder/.lint_skip
@@ -0,0 +1 @@
+CitationsMissing
diff --git a/data_managers/data_manager_fetch_gene_annotation/.lint_skip b/data_managers/data_manager_fetch_gene_annotation/.lint_skip
new file mode 100644
index 00000000000..3e5615e7bb9
--- /dev/null
+++ b/data_managers/data_manager_fetch_gene_annotation/.lint_skip
@@ -0,0 +1,3 @@
+CitationsMissing
+HelpEmpty
+TestsMissing
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
new file mode 100644
index 00000000000..46f5e08e85b
--- /dev/null
+++ b/data_managers/data_manager_fetch_genome_dbkeys_all_fasta/.lint_skip
@@ -0,0 +1 @@
+CitationsMissing
diff --git a/data_managers/data_manager_fetch_index_maf/.lint_skip b/data_managers/data_manager_fetch_index_maf/.lint_skip
new file mode 100644
index 00000000000..0518d2c178a
--- /dev/null
+++ b/data_managers/data_manager_fetch_index_maf/.lint_skip
@@ -0,0 +1,2 @@
+CitationsMissing
+TestsMissing
diff --git a/data_managers/data_manager_fetch_ncbi_taxonomy/.lint_skip b/data_managers/data_manager_fetch_ncbi_taxonomy/.lint_skip
new file mode 100644
index 00000000000..46f5e08e85b
--- /dev/null
+++ b/data_managers/data_manager_fetch_ncbi_taxonomy/.lint_skip
@@ -0,0 +1 @@
+CitationsMissing
diff --git a/data_managers/data_manager_gatk_picard_index_builder/.lint_skip b/data_managers/data_manager_gatk_picard_index_builder/.lint_skip
new file mode 100644
index 00000000000..0518d2c178a
--- /dev/null
+++ b/data_managers/data_manager_gatk_picard_index_builder/.lint_skip
@@ -0,0 +1,2 @@
+CitationsMissing
+TestsMissing
diff --git a/data_managers/data_manager_genomic_super_signature_ravmodels/.lint_skip b/data_managers/data_manager_genomic_super_signature_ravmodels/.lint_skip
new file mode 100644
index 00000000000..46f5e08e85b
--- /dev/null
+++ b/data_managers/data_manager_genomic_super_signature_ravmodels/.lint_skip
@@ -0,0 +1 @@
+CitationsMissing
diff --git a/data_managers/data_manager_gtdbtk_database_installer/.lint_skip b/data_managers/data_manager_gtdbtk_database_installer/.lint_skip
new file mode 100644
index 00000000000..7d044e96aea
--- /dev/null
+++ b/data_managers/data_manager_gtdbtk_database_installer/.lint_skip
@@ -0,0 +1 @@
+HelpEmpty
diff --git a/data_managers/data_manager_homer_preparsed/.lint_skip b/data_managers/data_manager_homer_preparsed/.lint_skip
new file mode 100644
index 00000000000..a85f2705a91
--- /dev/null
+++ b/data_managers/data_manager_homer_preparsed/.lint_skip
@@ -0,0 +1,3 @@
+CitationsMissing
+HelpEmpty
+XMLOrder
diff --git a/data_managers/data_manager_kallisto_index_builder/.lint_skip b/data_managers/data_manager_kallisto_index_builder/.lint_skip
new file mode 100644
index 00000000000..c779596e7cc
--- /dev/null
+++ b/data_managers/data_manager_kallisto_index_builder/.lint_skip
@@ -0,0 +1,2 @@
+HelpInvalidRST
+TestsMissing
diff --git a/data_managers/data_manager_malt_index_builder/.lint_skip b/data_managers/data_manager_malt_index_builder/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/data_managers/data_manager_malt_index_builder/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/data_managers/data_manager_manual/.lint_skip b/data_managers/data_manager_manual/.lint_skip
new file mode 100644
index 00000000000..e9fed198f57
--- /dev/null
+++ b/data_managers/data_manager_manual/.lint_skip
@@ -0,0 +1,3 @@
+CitationsMissing
+InputsSelectDynamicOptions
+XMLOrder
diff --git a/data_managers/data_manager_mash_sketch_builder/.lint_skip b/data_managers/data_manager_mash_sketch_builder/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/data_managers/data_manager_mash_sketch_builder/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/data_managers/data_manager_mothur_toolsuite/.lint_skip b/data_managers/data_manager_mothur_toolsuite/.lint_skip
new file mode 100644
index 00000000000..46f5e08e85b
--- /dev/null
+++ b/data_managers/data_manager_mothur_toolsuite/.lint_skip
@@ -0,0 +1 @@
+CitationsMissing
diff --git a/data_managers/data_manager_packaged_annotation_data/.lint_skip b/data_managers/data_manager_packaged_annotation_data/.lint_skip
new file mode 100644
index 00000000000..46f5e08e85b
--- /dev/null
+++ b/data_managers/data_manager_packaged_annotation_data/.lint_skip
@@ -0,0 +1 @@
+CitationsMissing
diff --git a/data_managers/data_manager_pangolin_data/.lint_skip b/data_managers/data_manager_pangolin_data/.lint_skip
new file mode 100644
index 00000000000..6a91ffad01c
--- /dev/null
+++ b/data_managers/data_manager_pangolin_data/.lint_skip
@@ -0,0 +1,2 @@
+RequirementVersionMissing
+XMLOrder
diff --git a/data_managers/data_manager_picard_index_builder/.lint_skip b/data_managers/data_manager_picard_index_builder/.lint_skip
new file mode 100644
index 00000000000..46f5e08e85b
--- /dev/null
+++ b/data_managers/data_manager_picard_index_builder/.lint_skip
@@ -0,0 +1 @@
+CitationsMissing
diff --git a/data_managers/data_manager_qiime_database_downloader/.lint_skip b/data_managers/data_manager_qiime_database_downloader/.lint_skip
new file mode 100644
index 00000000000..fd9005475bf
--- /dev/null
+++ b/data_managers/data_manager_qiime_database_downloader/.lint_skip
@@ -0,0 +1 @@
+TestsMissing
diff --git a/data_managers/data_manager_salmon_index_builder/.lint_skip b/data_managers/data_manager_salmon_index_builder/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/data_managers/data_manager_salmon_index_builder/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/data_managers/data_manager_sam_fasta_index_builder/.lint_skip b/data_managers/data_manager_sam_fasta_index_builder/.lint_skip
new file mode 100644
index 00000000000..46f5e08e85b
--- /dev/null
+++ b/data_managers/data_manager_sam_fasta_index_builder/.lint_skip
@@ -0,0 +1 @@
+CitationsMissing
diff --git a/data_managers/data_manager_selection_background/.lint_skip b/data_managers/data_manager_selection_background/.lint_skip
new file mode 100644
index 00000000000..d3a1493f388
--- /dev/null
+++ b/data_managers/data_manager_selection_background/.lint_skip
@@ -0,0 +1,2 @@
+CitationsMissing
+HelpEmpty
diff --git a/data_managers/data_manager_semibin/.lint_skip b/data_managers/data_manager_semibin/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/data_managers/data_manager_semibin/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/data_managers/data_manager_snpeff/.lint_skip b/data_managers/data_manager_snpeff/.lint_skip
new file mode 100644
index 00000000000..ac58e24884a
--- /dev/null
+++ b/data_managers/data_manager_snpeff/.lint_skip
@@ -0,0 +1,2 @@
+InputsMissing
+ToolVersionPEP404
diff --git a/data_managers/data_manager_star_index_builder/.lint_skip b/data_managers/data_manager_star_index_builder/.lint_skip
new file mode 100644
index 00000000000..dabcb8dc984
--- /dev/null
+++ b/data_managers/data_manager_star_index_builder/.lint_skip
@@ -0,0 +1 @@
+TestsParamInInputs
diff --git a/data_managers/data_manager_twobit_builder/.lint_skip b/data_managers/data_manager_twobit_builder/.lint_skip
new file mode 100644
index 00000000000..855dee9e6e0
--- /dev/null
+++ b/data_managers/data_manager_twobit_builder/.lint_skip
@@ -0,0 +1,2 @@
+CitationsMissing
+XMLOrder
diff --git a/data_managers/data_manager_vsnp_dnaprints/.lint_skip b/data_managers/data_manager_vsnp_dnaprints/.lint_skip
new file mode 100644
index 00000000000..f98c941cb66
--- /dev/null
+++ b/data_managers/data_manager_vsnp_dnaprints/.lint_skip
@@ -0,0 +1 @@
+CitationsNoValid
diff --git a/data_managers/data_manager_vsnp_excel/.lint_skip b/data_managers/data_manager_vsnp_excel/.lint_skip
new file mode 100644
index 00000000000..f98c941cb66
--- /dev/null
+++ b/data_managers/data_manager_vsnp_excel/.lint_skip
@@ -0,0 +1 @@
+CitationsNoValid
diff --git a/data_managers/data_manager_vsnp_genbank/.lint_skip b/data_managers/data_manager_vsnp_genbank/.lint_skip
new file mode 100644
index 00000000000..f98c941cb66
--- /dev/null
+++ b/data_managers/data_manager_vsnp_genbank/.lint_skip
@@ -0,0 +1 @@
+CitationsNoValid
diff --git a/tool_collections/cufflinks/cuffdiff/.lint_skip b/tool_collections/cufflinks/cuffdiff/.lint_skip
new file mode 100644
index 00000000000..cc60dd28c7b
--- /dev/null
+++ b/tool_collections/cufflinks/cuffdiff/.lint_skip
@@ -0,0 +1 @@
+TestsExpectNumOutputs
diff --git a/tool_collections/cufflinks/cuffnorm/.lint_skip b/tool_collections/cufflinks/cuffnorm/.lint_skip
new file mode 100644
index 00000000000..db401a876bb
--- /dev/null
+++ b/tool_collections/cufflinks/cuffnorm/.lint_skip
@@ -0,0 +1,2 @@
+OutputsLabelDuplicatedFilter
+OutputsNameDuplicated
diff --git a/tool_collections/fastx_toolkit/fastx_clipper/.lint_skip b/tool_collections/fastx_toolkit/fastx_clipper/.lint_skip
new file mode 100644
index 00000000000..f1a9e0e1123
--- /dev/null
+++ b/tool_collections/fastx_toolkit/fastx_clipper/.lint_skip
@@ -0,0 +1 @@
+InputsSelectOptionsDeprecatedAttr
diff --git a/tool_collections/galaxy_sequence_utils/fastq_combiner/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_combiner/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/tool_collections/galaxy_sequence_utils/fastq_combiner/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tool_collections/galaxy_sequence_utils/fastq_filter/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_filter/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/tool_collections/galaxy_sequence_utils/fastq_filter/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tool_collections/galaxy_sequence_utils/fastq_groomer/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_groomer/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/tool_collections/galaxy_sequence_utils/fastq_groomer/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tool_collections/galaxy_sequence_utils/fastq_manipulation/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_manipulation/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/tool_collections/galaxy_sequence_utils/fastq_manipulation/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
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
new file mode 100644
index 00000000000..5a3d475d5d1
--- /dev/null
+++ b/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer/.lint_skip
@@ -0,0 +1,3 @@
+OutputsLabelDuplicatedFilter
+TestsExpectNumOutputs
+XMLOrder
diff --git a/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tool_collections/galaxy_sequence_utils/fastq_stats/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_stats/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/tool_collections/galaxy_sequence_utils/fastq_stats/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tool_collections/galaxy_sequence_utils/fastq_to_tabular/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_to_tabular/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/tool_collections/galaxy_sequence_utils/fastq_to_tabular/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tool_collections/galaxy_sequence_utils/fastq_trimmer/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_trimmer/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/tool_collections/galaxy_sequence_utils/fastq_trimmer/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tool_collections/galaxy_sequence_utils/fastqtofasta/.lint_skip b/tool_collections/galaxy_sequence_utils/fastqtofasta/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/tool_collections/galaxy_sequence_utils/fastqtofasta/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tool_collections/galaxy_sequence_utils/tabular_to_fastq/.lint_skip b/tool_collections/galaxy_sequence_utils/tabular_to_fastq/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/tool_collections/galaxy_sequence_utils/tabular_to_fastq/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tool_collections/snpeff/.lint_skip b/tool_collections/snpeff/.lint_skip
new file mode 100644
index 00000000000..a505b27b40f
--- /dev/null
+++ b/tool_collections/snpeff/.lint_skip
@@ -0,0 +1,3 @@
+InputsDataOptionsFilterAttribFiltersType
+InputsDataOptionsFiltersRef
+TestsExpectNumOutputs
diff --git a/tool_collections/snpsift/snpsift/.lint_skip b/tool_collections/snpsift/snpsift/.lint_skip
new file mode 100644
index 00000000000..039bcb6e720
--- /dev/null
+++ b/tool_collections/snpsift/snpsift/.lint_skip
@@ -0,0 +1,2 @@
+TestsMissing
+XMLOrder
diff --git a/tool_collections/snpsift/snpsift_dbnsfp/.lint_skip b/tool_collections/snpsift/snpsift_dbnsfp/.lint_skip
new file mode 100644
index 00000000000..fd9005475bf
--- /dev/null
+++ b/tool_collections/snpsift/snpsift_dbnsfp/.lint_skip
@@ -0,0 +1 @@
+TestsMissing
diff --git a/tool_collections/snpsift/snpsift_genesets/.lint_skip b/tool_collections/snpsift/snpsift_genesets/.lint_skip
new file mode 100644
index 00000000000..fd9005475bf
--- /dev/null
+++ b/tool_collections/snpsift/snpsift_genesets/.lint_skip
@@ -0,0 +1 @@
+TestsMissing
diff --git a/tool_collections/vcflib/vcffilter/.lint_skip b/tool_collections/vcflib/vcffilter/.lint_skip
new file mode 100644
index 00000000000..e7d00398ee9
--- /dev/null
+++ b/tool_collections/vcflib/vcffilter/.lint_skip
@@ -0,0 +1 @@
+InputsNameRedundantArgument
diff --git a/tool_collections/vcflib/vcfsort/.lint_skip b/tool_collections/vcflib/vcfsort/.lint_skip
new file mode 100644
index 00000000000..46f5e08e85b
--- /dev/null
+++ b/tool_collections/vcflib/vcfsort/.lint_skip
@@ -0,0 +1 @@
+CitationsMissing
diff --git a/tools/abricate/.lint_skip b/tools/abricate/.lint_skip
new file mode 100644
index 00000000000..0332c4d534d
--- /dev/null
+++ b/tools/abricate/.lint_skip
@@ -0,0 +1,2 @@
+InputsMissing
+XMLOrder
diff --git a/tools/add_input_name_as_column/.lint_skip b/tools/add_input_name_as_column/.lint_skip
new file mode 100644
index 00000000000..46f5e08e85b
--- /dev/null
+++ b/tools/add_input_name_as_column/.lint_skip
@@ -0,0 +1 @@
+CitationsMissing
diff --git a/tools/allegro/.lint_skip b/tools/allegro/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/tools/allegro/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tools/amplican/.lint_skip b/tools/amplican/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/tools/amplican/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tools/arriba/.lint_skip b/tools/arriba/.lint_skip
new file mode 100644
index 00000000000..1d303e867c4
--- /dev/null
+++ b/tools/arriba/.lint_skip
@@ -0,0 +1 @@
+ValidatorExpression
diff --git a/tools/art/.lint_skip b/tools/art/.lint_skip
new file mode 100644
index 00000000000..de67bcbc665
--- /dev/null
+++ b/tools/art/.lint_skip
@@ -0,0 +1,4 @@
+ConditionalParamTypeBool
+OutputsLabelDuplicatedFilter
+TestsExpectNumOutputs
+XMLOrder
diff --git a/tools/augustus/.lint_skip b/tools/augustus/.lint_skip
new file mode 100644
index 00000000000..60dcaf138b5
--- /dev/null
+++ b/tools/augustus/.lint_skip
@@ -0,0 +1,5 @@
+InputsNameRedundantArgument
+InputsSelectOptionDuplicateText
+InputsSelectOptionDuplicateValue
+TestsExpectNumOutputs
+XMLOrder
diff --git a/tools/b2btools/.lint_skip b/tools/b2btools/.lint_skip
new file mode 100644
index 00000000000..e7d00398ee9
--- /dev/null
+++ b/tools/b2btools/.lint_skip
@@ -0,0 +1 @@
+InputsNameRedundantArgument
diff --git a/tools/bamutil/.lint_skip b/tools/bamutil/.lint_skip
new file mode 100644
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+InputsNameRedundantArgument
diff --git a/tools/strelka/.lint_skip b/tools/strelka/.lint_skip
new file mode 100644
index 00000000000..e7d00398ee9
--- /dev/null
+++ b/tools/strelka/.lint_skip
@@ -0,0 +1 @@
+InputsNameRedundantArgument
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new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/tools/structure/.lint_skip
@@ -0,0 +1 @@
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diff --git a/tools/structureharvester/.lint_skip b/tools/structureharvester/.lint_skip
new file mode 100644
index 00000000000..4d97c7e23e6
--- /dev/null
+++ b/tools/structureharvester/.lint_skip
@@ -0,0 +1,2 @@
+InputsNameDuplicateOutput
+TestsExpectNumOutputs
diff --git a/tools/swift/.lint_skip b/tools/swift/.lint_skip
new file mode 100644
index 00000000000..c4d48dac9f2
--- /dev/null
+++ b/tools/swift/.lint_skip
@@ -0,0 +1,2 @@
+InputsNameRedundantArgument
+TestsExpectNumOutputs
diff --git a/tools/table_compute/.lint_skip b/tools/table_compute/.lint_skip
new file mode 100644
index 00000000000..b5212db9362
--- /dev/null
+++ b/tools/table_compute/.lint_skip
@@ -0,0 +1,2 @@
+CitationsNoValid
+TestsExpectNumOutputsFailing
diff --git a/tools/tag_pileup_frequency/.lint_skip b/tools/tag_pileup_frequency/.lint_skip
new file mode 100644
index 00000000000..cc60dd28c7b
--- /dev/null
+++ b/tools/tag_pileup_frequency/.lint_skip
@@ -0,0 +1 @@
+TestsExpectNumOutputs
diff --git a/tools/tasmanian_mismatch/.lint_skip b/tools/tasmanian_mismatch/.lint_skip
new file mode 100644
index 00000000000..cc60dd28c7b
--- /dev/null
+++ b/tools/tasmanian_mismatch/.lint_skip
@@ -0,0 +1 @@
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diff --git a/tools/tbl2gff3/.lint_skip b/tools/tbl2gff3/.lint_skip
new file mode 100644
index 00000000000..f98c941cb66
--- /dev/null
+++ b/tools/tbl2gff3/.lint_skip
@@ -0,0 +1 @@
+CitationsNoValid
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new file mode 100644
index 00000000000..5a3d475d5d1
--- /dev/null
+++ b/tools/telescope/.lint_skip
@@ -0,0 +1,3 @@
+OutputsLabelDuplicatedFilter
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diff --git a/tools/tetyper/.lint_skip b/tools/tetyper/.lint_skip
new file mode 100644
index 00000000000..cc60dd28c7b
--- /dev/null
+++ b/tools/tetyper/.lint_skip
@@ -0,0 +1 @@
+TestsExpectNumOutputs
diff --git a/tools/tn93/.lint_skip b/tools/tn93/.lint_skip
new file mode 100644
index 00000000000..232ad9b2230
--- /dev/null
+++ b/tools/tn93/.lint_skip
@@ -0,0 +1,2 @@
+HelpInvalidRST
+OutputsLabelDuplicatedFilter
diff --git a/tools/transdecoder/.lint_skip b/tools/transdecoder/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/tools/transdecoder/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tools/transit/.lint_skip b/tools/transit/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/tools/transit/.lint_skip
@@ -0,0 +1 @@
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diff --git a/tools/trinotate/.lint_skip b/tools/trinotate/.lint_skip
new file mode 100644
index 00000000000..ee3065a51c9
--- /dev/null
+++ b/tools/trinotate/.lint_skip
@@ -0,0 +1,2 @@
+TestsExpectNumOutputs
+XMLOrder
diff --git a/tools/tsne/.lint_skip b/tools/tsne/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/tools/tsne/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tools/tximport/.lint_skip b/tools/tximport/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/tools/tximport/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tools/ucsc_blat/.lint_skip b/tools/ucsc_blat/.lint_skip
new file mode 100644
index 00000000000..a1cf37844af
--- /dev/null
+++ b/tools/ucsc_blat/.lint_skip
@@ -0,0 +1 @@
+TestsOutputCompareAttrib
diff --git a/tools/ucsc_tools/fasplit/.lint_skip b/tools/ucsc_tools/fasplit/.lint_skip
new file mode 100644
index 00000000000..af4cf5ec3d4
--- /dev/null
+++ b/tools/ucsc_tools/fasplit/.lint_skip
@@ -0,0 +1,2 @@
+CitationsNoValid
+XMLOrder
diff --git a/tools/ucsc_tools/twobittofa/.lint_skip b/tools/ucsc_tools/twobittofa/.lint_skip
new file mode 100644
index 00000000000..af4cf5ec3d4
--- /dev/null
+++ b/tools/ucsc_tools/twobittofa/.lint_skip
@@ -0,0 +1,2 @@
+CitationsNoValid
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diff --git a/tools/umi_tools/.lint_skip b/tools/umi_tools/.lint_skip
new file mode 100644
index 00000000000..dc4adbb445e
--- /dev/null
+++ b/tools/umi_tools/.lint_skip
@@ -0,0 +1,6 @@
+CommandTODO
+InputsNameRedundantArgument
+OutputsLabelDuplicatedFilter
+TestsExpectNumOutputs
+TestsParamInInputs
+XMLOrder
diff --git a/tools/varscan/.lint_skip b/tools/varscan/.lint_skip
new file mode 100644
index 00000000000..e7d00398ee9
--- /dev/null
+++ b/tools/varscan/.lint_skip
@@ -0,0 +1 @@
+InputsNameRedundantArgument
diff --git a/tools/vcf2maf/.lint_skip b/tools/vcf2maf/.lint_skip
new file mode 100644
index 00000000000..dabcb8dc984
--- /dev/null
+++ b/tools/vcf2maf/.lint_skip
@@ -0,0 +1 @@
+TestsParamInInputs
diff --git a/tools/velvet/.lint_skip b/tools/velvet/.lint_skip
new file mode 100644
index 00000000000..a68d017209e
--- /dev/null
+++ b/tools/velvet/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tools/vg/.lint_skip b/tools/vg/.lint_skip
new file mode 100644
index 00000000000..02e7f1dcf79
--- /dev/null
+++ b/tools/vg/.lint_skip
@@ -0,0 +1,2 @@
+CitationsNoValid
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diff --git a/tools/vsearch/.lint_skip b/tools/vsearch/.lint_skip
new file mode 100644
index 00000000000..de4e58e9ed1
--- /dev/null
+++ b/tools/vsearch/.lint_skip
@@ -0,0 +1,3 @@
+InputsSelectOptionDuplicateText
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+XMLOrder
diff --git a/tools/vsnp/.lint_skip b/tools/vsnp/.lint_skip
new file mode 100644
index 00000000000..dabcb8dc984
--- /dev/null
+++ b/tools/vsnp/.lint_skip
@@ -0,0 +1 @@
+TestsParamInInputs
diff --git a/tools/winnowmap/.lint_skip b/tools/winnowmap/.lint_skip
new file mode 100644
index 00000000000..e7d00398ee9
--- /dev/null
+++ b/tools/winnowmap/.lint_skip
@@ -0,0 +1 @@
+InputsNameRedundantArgument
diff --git a/tools/xpath/.lint_skip b/tools/xpath/.lint_skip
new file mode 100644
index 00000000000..f98c941cb66
--- /dev/null
+++ b/tools/xpath/.lint_skip
@@ -0,0 +1 @@
+CitationsNoValid