Merge pull request galaxyproject#6184 from bernt-matthias/topic/skip_…

…lint Add linter exceptions for all linters that are currently failing
pavanvidem · Sep 5, 2024 · d7032f8 · d7032f8
2 parents 5706be8 + 9882d51
commit d7032f8
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Showing 269 changed files with 436 additions and 12 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -0,0 +1 @@
+HelpEmpty
diff --git a/data_managers/data_manager_homer_preparsed/.lint_skip 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
@@ -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
@@ -0,0 +1 @@
+XMLOrder
diff --git a/data_managers/data_manager_manual/.lint_skip 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
@@ -0,0 +1 @@
+XMLOrder
diff --git a/data_managers/data_manager_mothur_toolsuite/.lint_skip 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
@@ -0,0 +1 @@
+CitationsMissing
diff --git a/data_managers/data_manager_pangolin_data/.lint_skip 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
@@ -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
@@ -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
@@ -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
@@ -0,0 +1 @@
+CitationsMissing
diff --git a/data_managers/data_manager_selection_background/.lint_skip 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
@@ -0,0 +1 @@
+XMLOrder
diff --git a/data_managers/data_manager_snpeff/.lint_skip 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
@@ -0,0 +1 @@
+TestsParamInInputs
diff --git a/data_managers/data_manager_twobit_builder/.lint_skip 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
@@ -0,0 +1 @@
+CitationsNoValid
diff --git a/data_managers/data_manager_vsnp_excel/.lint_skip 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
@@ -0,0 +1 @@
+CitationsNoValid
diff --git a/tool_collections/cufflinks/cuffdiff/.lint_skip 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tool_collections/galaxy_sequence_utils/fastqtofasta/.lint_skip 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
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tool_collections/snpeff/.lint_skip 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
@@ -0,0 +1,2 @@
+TestsMissing
+XMLOrder
diff --git a/tool_collections/snpsift/snpsift_dbnsfp/.lint_skip 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
@@ -0,0 +1 @@
+TestsMissing
diff --git a/tool_collections/vcflib/vcffilter/.lint_skip 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
@@ -0,0 +1 @@
+CitationsMissing
diff --git a/tools/abricate/.lint_skip 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
@@ -0,0 +1 @@
+CitationsMissing
diff --git a/tools/allegro/.lint_skip b/tools/allegro/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tools/amplican/.lint_skip b/tools/amplican/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tools/arriba/.lint_skip b/tools/arriba/.lint_skip
@@ -0,0 +1 @@
+ValidatorExpression
diff --git a/tools/art/.lint_skip 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
@@ -0,0 +1,5 @@
+InputsNameRedundantArgument
+InputsSelectOptionDuplicateText
+InputsSelectOptionDuplicateValue
+TestsExpectNumOutputs
+XMLOrder
diff --git a/tools/b2btools/.lint_skip b/tools/b2btools/.lint_skip
@@ -0,0 +1 @@
+InputsNameRedundantArgument
diff --git a/tools/bamutil/.lint_skip b/tools/bamutil/.lint_skip
@@ -0,0 +1,2 @@
+OutputsLabelDuplicatedFilter
+XMLOrder
diff --git a/tools/barcode_splitter/.lint_skip b/tools/barcode_splitter/.lint_skip
@@ -0,0 +1,2 @@
+ConditionalWhenMissing
+TestsExpectNumOutputs
diff --git a/tools/baredsc/.lint_skip b/tools/baredsc/.lint_skip
@@ -0,0 +1 @@
+EDAMTermsValid
diff --git a/tools/barrnap/.lint_skip b/tools/barrnap/.lint_skip
@@ -0,0 +1 @@
+TestsExpectNumOutputs
diff --git a/tools/bctools/.lint_skip b/tools/bctools/.lint_skip
@@ -0,0 +1,3 @@
+InputsNameRedundantArgument
+OutputsLabelDuplicatedNoFilter
+ToolVersionPEP404
diff --git a/tools/beagle/.lint_skip b/tools/beagle/.lint_skip
@@ -0,0 +1 @@
+ToolVersionPEP404
diff --git a/tools/bioperl/.lint_skip b/tools/bioperl/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tools/blastxml_to_gapped_gff3/.lint_skip b/tools/blastxml_to_gapped_gff3/.lint_skip
@@ -0,0 +1 @@
+CitationsNoValid
diff --git a/tools/bowtie2/.lint_skip b/tools/bowtie2/.lint_skip
@@ -0,0 +1 @@
+ConditionalParamTypeBool
diff --git a/tools/breseq/.lint_skip b/tools/breseq/.lint_skip
@@ -0,0 +1,3 @@
+InputsNameRedundantArgument
+TestsExpectNumOutputs
+XMLOrder
diff --git a/tools/bwa/.lint_skip b/tools/bwa/.lint_skip
@@ -0,0 +1 @@
+ConditionalParamTypeBool
diff --git a/tools/bwa_mem2/.lint_skip b/tools/bwa_mem2/.lint_skip
@@ -0,0 +1,2 @@
+ConditionalParamTypeBool
+XMLOrder
diff --git a/tools/cat/.lint_skip b/tools/cat/.lint_skip
@@ -0,0 +1,2 @@
+InputsMissing
+TestsMissing
diff --git a/tools/cdhit/.lint_skip b/tools/cdhit/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tools/charts/.lint_skip b/tools/charts/.lint_skip
@@ -0,0 +1,2 @@
+CitationsMissing
+HelpMissing
diff --git a/tools/checkm/.lint_skip b/tools/checkm/.lint_skip
@@ -0,0 +1,2 @@
+OutputsLabelDuplicatedFilter
+OutputsNameDuplicated
diff --git a/tools/cherri/.lint_skip b/tools/cherri/.lint_skip
@@ -0,0 +1 @@
+CitationsNoValid
diff --git a/tools/chira/.lint_skip b/tools/chira/.lint_skip
@@ -0,0 +1 @@
+CitationsNoValid
diff --git a/tools/circexplorer2/.lint_skip b/tools/circexplorer2/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tools/circos/.lint_skip b/tools/circos/.lint_skip
@@ -0,0 +1 @@
+TestsExpectNumOutputs
diff --git a/tools/cite_seq_count/.lint_skip b/tools/cite_seq_count/.lint_skip
@@ -0,0 +1 @@
+EDAMTermsValid
diff --git a/tools/colibread/.lint_skip b/tools/colibread/.lint_skip
@@ -0,0 +1,3 @@
+InputsNameRedundantArgument
+TestsExpectNumOutputs
+TestsParamInInputs
diff --git a/tools/collection_column_join/.lint_skip b/tools/collection_column_join/.lint_skip
@@ -0,0 +1,3 @@
+CitationsNoValid
+OutputsLabelDuplicatedFilter
+TestsExpectNumOutputs
diff --git a/tools/collection_element_identifiers/.lint_skip b/tools/collection_element_identifiers/.lint_skip
@@ -0,0 +1 @@
+CitationsNoValid
diff --git a/tools/column_maker/.lint_skip b/tools/column_maker/.lint_skip
@@ -0,0 +1 @@
+CitationsNoValid
diff --git a/tools/column_order_header_sort/.lint_skip b/tools/column_order_header_sort/.lint_skip
@@ -0,0 +1 @@
+CitationsNoValid
diff --git a/tools/column_remove_by_header/.lint_skip b/tools/column_remove_by_header/.lint_skip
@@ -0,0 +1 @@
+CitationsNoValid
diff --git a/tools/compress_file/.lint_skip b/tools/compress_file/.lint_skip
@@ -0,0 +1 @@
+CitationsNoValid
diff --git a/tools/crossmap/.lint_skip b/tools/crossmap/.lint_skip
@@ -0,0 +1 @@
+TestsExpectNumOutputs
diff --git a/tools/cutesv/.lint_skip b/tools/cutesv/.lint_skip
@@ -0,0 +1,2 @@
+TestsParamInInputs
+XMLOrder
diff --git a/tools/cwpair2/.lint_skip b/tools/cwpair2/.lint_skip
@@ -0,0 +1 @@
+TestsExpectNumOutputs
diff --git a/tools/decontaminator/.lint_skip b/tools/decontaminator/.lint_skip
@@ -0,0 +1 @@
+CitationsMissing
diff --git a/tools/deg_annotate/.lint_skip b/tools/deg_annotate/.lint_skip
@@ -0,0 +1 @@
+CitationsMissing
diff --git a/tools/delly/.lint_skip b/tools/delly/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tools/diamond/.lint_skip b/tools/diamond/.lint_skip
@@ -0,0 +1,2 @@
+InputsNameRedundantArgument
+OutputsLabelDuplicatedFilter
diff --git a/tools/disco/.lint_skip b/tools/disco/.lint_skip
@@ -0,0 +1,4 @@
+CitationsNoValid
+InputsNameDuplicateOutput
+TestsExpectNumOutputs
+XMLOrder
diff --git a/tools/dnaweaver/.lint_skip b/tools/dnaweaver/.lint_skip
@@ -0,0 +1 @@
+CitationsMissing
diff --git a/tools/dropletutils/.lint_skip b/tools/dropletutils/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tools/emboss_5/.lint_skip b/tools/emboss_5/.lint_skip
@@ -0,0 +1,6 @@
+InputsSelectOptionDuplicateText
+OutputsLabelDuplicatedNoFilter
+TestsMissing
+TestsParamInInputs
+ToolIDWhitespace
+XMLOrder
diff --git a/tools/exonerate/.lint_skip b/tools/exonerate/.lint_skip
@@ -0,0 +1,2 @@
+TestsExpectNumOutputs
+XMLOrder
diff --git a/tools/extract_genomic_dna/.lint_skip b/tools/extract_genomic_dna/.lint_skip
@@ -0,0 +1 @@
+ToolIDWhitespace
diff --git a/tools/fasta_nucleotide_color_plot/.lint_skip b/tools/fasta_nucleotide_color_plot/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tools/fasttree/.lint_skip b/tools/fasttree/.lint_skip
@@ -0,0 +1,4 @@
+InputsBoolDistinctValues
+InputsNameRedundantArgument
+TestsExpectNumOutputs
+XMLOrder
diff --git a/tools/fermikit/.lint_skip b/tools/fermikit/.lint_skip
@@ -0,0 +1 @@
+ToolVersionPEP404
diff --git a/tools/fgsea/.lint_skip b/tools/fgsea/.lint_skip
@@ -0,0 +1 @@
+TestsExpectNumOutputs
diff --git a/tools/flair/.lint_skip b/tools/flair/.lint_skip
@@ -0,0 +1 @@
+InputsNameRedundantArgument
diff --git a/tools/flash/.lint_skip b/tools/flash/.lint_skip
@@ -0,0 +1,4 @@
+InputsBoolDistinctValues
+InputsNameRedundantArgument
+OutputsLabelDuplicatedFilter
+XMLOrder
diff --git a/tools/fraggenescan/.lint_skip b/tools/fraggenescan/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tools/freebayes/.lint_skip b/tools/freebayes/.lint_skip
@@ -0,0 +1,3 @@
+InputsNameRedundantArgument
+TestsExpectNumOutputs
+XMLOrder
diff --git a/tools/gatk4/.lint_skip b/tools/gatk4/.lint_skip
@@ -0,0 +1,5 @@
+InputsNameDuplicate
+InputsNameRedundantArgument
+TestsExpectNumOutputs
+TestsParamInInputs
+ToolVersionPEP404
diff --git a/tools/gecko/.lint_skip b/tools/gecko/.lint_skip
@@ -0,0 +1 @@
+ConditionalWhenMissing
diff --git a/tools/gemini/.lint_skip b/tools/gemini/.lint_skip
@@ -0,0 +1,5 @@
+InputsDataOptionsFilterAttribFiltersType
+InputsDataOptionsFiltersRef
+InputsDataOptionsFiltersType
+InputsNameRedundantArgument
+XMLOrder
diff --git a/tools/genehunter_modscore/.lint_skip b/tools/genehunter_modscore/.lint_skip
@@ -0,0 +1 @@
+ConditionalParamTypeBool
diff --git a/tools/genomic_super_signature/.lint_skip b/tools/genomic_super_signature/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tools/gfa_to_fa/.lint_skip b/tools/gfa_to_fa/.lint_skip
@@ -0,0 +1 @@
+CitationsMissing
diff --git a/tools/gffcompare/.lint_skip b/tools/gffcompare/.lint_skip
@@ -0,0 +1,2 @@
+OutputsLabelDuplicatedFilter
+TestsOutputCompareAttrib
diff --git a/tools/ggplot2/.lint_skip b/tools/ggplot2/.lint_skip
@@ -0,0 +1,4 @@
+CitationsNoValid
+InputsNameDuplicate
+TestsExpectNumOutputs
+XMLOrder
diff --git a/tools/ggupset/.lint_skip b/tools/ggupset/.lint_skip
@@ -0,0 +1 @@
+CitationsMissing
diff --git a/tools/glimmer/.lint_skip b/tools/glimmer/.lint_skip
@@ -0,0 +1,5 @@
+CommandTODO
+InputsBoolDistinctValues
+OutputsLabelDuplicatedNoFilter
+TestsExpectNumOutputs
+XMLOrder
diff --git a/tools/goenrichment/.lint_skip b/tools/goenrichment/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tools/goseq/.lint_skip b/tools/goseq/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tools/gprofiler/.lint_skip b/tools/gprofiler/.lint_skip
@@ -0,0 +1 @@
+TestsExpectNumOutputs
diff --git a/tools/gvcftools/.lint_skip b/tools/gvcftools/.lint_skip
@@ -0,0 +1 @@
+InputsNameRedundantArgument
diff --git a/tools/hansel/.lint_skip b/tools/hansel/.lint_skip
@@ -0,0 +1 @@
+TestsParamInInputs
diff --git a/tools/happy/.lint_skip b/tools/happy/.lint_skip
@@ -0,0 +1 @@
+CitationsMissing
diff --git a/tools/hicstuff/.lint_skip b/tools/hicstuff/.lint_skip
@@ -0,0 +1 @@
+OutputsLabelDuplicatedNoFilter
diff --git a/tools/hisat2/.lint_skip b/tools/hisat2/.lint_skip
@@ -0,0 +1,2 @@
+InputsNameRedundantArgument
+TestsExpectNumOutputs
diff --git a/tools/hivclustering/.lint_skip b/tools/hivclustering/.lint_skip
@@ -0,0 +1,2 @@
+InputsNameRedundantArgument
+TestsParamInInputs
diff --git a/tools/hybpiper/.lint_skip b/tools/hybpiper/.lint_skip
@@ -0,0 +1 @@
+XSD
diff --git a/tools/hyphy/.lint_skip b/tools/hyphy/.lint_skip
@@ -0,0 +1 @@
+TestsExpectNumOutputs
diff --git a/tools/hypo/.lint_skip b/tools/hypo/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tools/idba_ud/.lint_skip b/tools/idba_ud/.lint_skip
@@ -0,0 +1 @@
+XMLOrder
diff --git a/tools/idr/.lint_skip b/tools/idr/.lint_skip
@@ -0,0 +1,2 @@
+InputsNameRedundantArgument
+TestsExpectNumOutputs
diff --git a/tools/idr_download/.lint_skip b/tools/idr_download/.lint_skip
@@ -0,0 +1 @@
+TestsExpectNumOutputs
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		OutputsLabelDuplicatedFilter
		OutputsNameDuplicated
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		InputsNameRedundantArgument
		OutputsLabelDuplicatedFilter
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		OutputsLabelDuplicatedFilter
		TestsOutputCompareAttrib
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		InputsNameRedundantArgument
		TestsExpectNumOutputs
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		InputsNameRedundantArgument
		TestsParamInInputs