Merge pull request #627 from nsoranzo/deprecate_annotation_profiler

Deprecate ``annotation_profiler`` tool
galaxyproject · Sep 27, 2024 · b0b248a · b0b248a
2 parents ad21465 + ec9bc53
commit b0b248a
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diff --git a/.tt_skip b/.tt_skip
@@ -14,7 +14,6 @@ tool_collections/vcftools/vcftools_isec
 tool_collections/vcftools/vcftools_merge
 tool_collections/vcftools/vcftools_slice
 tool_collections/vcftools/vcftools_subset
-tools/annotation_profiler
 tools/best_regression_subsets
 tools/blat_coverage_report
 tools/blat_mapping

diff --git a/tools/annotation_profiler/.shed.yml → ...cated/tools/annotation_profiler/.shed.yml b/tools/annotation_profiler/.shed.yml → ...cated/tools/annotation_profiler/.shed.yml
diff --git a/...notation_profiler/annotation_profiler.xml → ...notation_profiler/annotation_profiler.xml b/...notation_profiler/annotation_profiler.xml → ...notation_profiler/annotation_profiler.xml
diff --git a/...filer/annotation_profiler_for_interval.py → ...filer/annotation_profiler_for_interval.py b/...filer/annotation_profiler_for_interval.py → ...filer/annotation_profiler_for_interval.py
diff --git a/tools/annotation_profiler/scripts/README.txt → ...ls/annotation_profiler/scripts/README.txt b/tools/annotation_profiler/scripts/README.txt → ...ls/annotation_profiler/scripts/README.txt
diff --git a/...profiler/scripts/build_profile_indexes.py → ...profiler/scripts/build_profile_indexes.py b/...profiler/scripts/build_profile_indexes.py → ...profiler/scripts/build_profile_indexes.py
diff --git a/tools/annotation_profiler/test-data/3.bed → ...tools/annotation_profiler/test-data/3.bed b/tools/annotation_profiler/test-data/3.bed → ...tools/annotation_profiler/test-data/3.bed
diff --git a/tools/annotation_profiler/test-data/4.bed → ...tools/annotation_profiler/test-data/4.bed b/tools/annotation_profiler/test-data/4.bed → ...tools/annotation_profiler/test-data/4.bed
diff --git a/...filer/test-data/annotation_profiler_1.out → ...filer/test-data/annotation_profiler_1.out b/...filer/test-data/annotation_profiler_1.out → ...filer/test-data/annotation_profiler_1.out
diff --git a/...filer/test-data/annotation_profiler_2.out → ...filer/test-data/annotation_profiler_2.out b/...filer/test-data/annotation_profiler_2.out → ...filer/test-data/annotation_profiler_2.out
diff --git a/...ta/annotation_profiler_options.xml.sample → ...ta/annotation_profiler_options.xml.sample b/...ta/annotation_profiler_options.xml.sample → ...ta/annotation_profiler_options.xml.sample
diff --git a/...notation_profiler_valid_builds.txt.sample → ...notation_profiler_valid_builds.txt.sample b/...notation_profiler_valid_builds.txt.sample → ...notation_profiler_valid_builds.txt.sample
diff --git a/...annotation_profiler/tool_dependencies.xml → ...annotation_profiler/tool_dependencies.xml b/...annotation_profiler/tool_dependencies.xml → ...annotation_profiler/tool_dependencies.xml