| Previous changeset 20:974bb00b2f43 (2024-10-18) Next changeset 22:c5541bfb8feb (2024-10-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 90275e51aa271edacdd9d277c441e38e99502c53 |
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added:
old_output.json test-data/krumsiek11_ranked_gene_groups.h5ad test-data/test.h5ad |
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| diff -r 974bb00b2f43 -r acc4732fae0b old_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/old_output.json Mon Oct 28 18:06:52 2024 +0000 |
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| b'@@ -0,0 +1,1 @@\n+{"version": "0.1", "tests": [{"id": "functional.test_toolbox.TestForTool_scanpy_plot.test_tool_000000", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy0", "test_index": 0, "time_seconds": 28.03529191017151, "inputs": {"adata": {"src": "hda", "id": "2891970512fa2d5a"}, "advanced_common|show_log": true, "format": "png", "method|method": "pl.scatter", "method|plot|color_map": "inferno", "method|plot|frameon": true, "method|plot|legend_fontsize": "1", "method|plot|legend_fontweight": "normal", "method|plot|legend_loc": "right margin", "method|plot|palette": "inferno", "method|plot|projection": "2d", "method|plot|size": "1", "method|sort_order": true, "method|type|basis": "umap", "method|type|color": "HES4", "method|type|type": "basis", "method|use_raw": true}, "job": {"command_line": "cp \'/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/files/7/b/c/dataset_7bc02b2c-0d82-4456-abcd-7ec123a4006d.dat\' \'anndata.h5ad\' && cat \'/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/2/configs/tmpinudjtrk\' > \'/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/files/b/a/7/dataset_ba72e443-4078-464d-8f69-93ff16fb341d.dat\' && python \'/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/job_working_directory/000/2/configs/tmpinudjtrk\' >> \'/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/files/b/a/7/dataset_ba72e443-4078-464d-8f69-93ff16fb341d.dat\' && ls . >> \'/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpn0nfhjgd/files/b/a/7/dataset_ba72e443-4078-464d-8f69-93ff16fb341d.dat\' && touch \'anndata_info.txt\' && cat \'anndata_info.txt\' | sed -r \'1 s|AnnData object with (.+) = (.*)\\\\s*|\\\\1: \\\\2|g\' | sed \\"s|\'||g\\" | sed -r \'s|^\\\\s*(.*):\\\\s(.*)|[\\\\1]\\\\n- \\\\2|g\' | sed \'s|, |\\\\n- |g\'", "command_version": "scanpy version: 1.7.1\\n", "create_time": "2021-03-15T16:18:49.439040", "exit_code": 0, "external_id": "46459", "galaxy_version": "21.01", "history_id": "2891970512fa2d5a", "id": "5729865256bc2525", "inputs": {"adata": {"id": "2891970512fa2d5a", "src": "hda", "uuid": "7bc02b2c-0d82-4456-abcd-7ec123a4006d"}}, "job_messages": [], "job_metrics": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "outputs": {"hidden_output": {"id": "54f2a3a23292eb07", "src": "hda", "uuid": "ba72e443-4078-464d-8f69-93ff16fb341d"}, "out_png": {"id": "5729865256bc2525", "src": "hda", "uuid": "79c9b4aa-c8ce-4f05-a32c-918bd718908c"}}, "params": {"__input_ext": "\\"input\\"", "advanced_common": "{\\"show_log\\": \\"true\\"}", "chromInfo": "\\"/Users/mvandenb/src/galaxy/tool-data/shared/ucsc/chrom/?.len\\"", "dbkey": "\\"?\\"", "format": "\\"png\\"", "method": "{\\"__current_case__\\": 0, \\"groups\\": \\"\\", \\"method\\": \\"pl.scatter\\", \\"plot\\": {\\"color_map\\": \\"inferno\\", \\"components\\": [], \\"frameon\\": \\"true\\", \\"legend_fontsize\\": \\"1\\", \\"legend_fontweight\\": \\"normal\\", \\"legend_loc\\": \\"right margin\\", \\"palette\\": \\"inferno\\", \\"projection\\": \\"2d\\", \\"size\\": \\"1.0\\", \\"title\\": \\"\\"}, \\"sort_order\\": \\"true\\", \\"type\\": {\\"__current_case__\\": 1, \\"basis\\": \\"umap\\", \\"color\\": \\"HES4\\", \\"type\\": \\"basis\\"}, \\"use_raw\\": \\"true\\"}"}, "state": "ok", "stderr": "WARNING: saving figure to file umap.png\\n", "stdout": "", "tool_id": "scanpy_plot", "tool_stderr": "WARNING: saving figure to file umap.png\\n", "tool_stdout": "", "update_time": "2021-03-15T16:19:05.199885", "user_email": "test@bx.psu.edu"}, "status": "success"}}, {"id": "functional.test_toolbox.TestForTool_scanpy_plot.test_tool_000009", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy0", "test_index": 9, "time_seconds": 21.56184482574463, "inputs": {"adata": {"src": "hda", "id": "8155e4b4bf1581ff"}, "advanced_common|show_log": true, "format": "png", "method|highly_variable_genes": true, "method|log": false, "method|method": "pl.highly_variable_genes"}, "job": {"command_line": "cp \'/private/var/folders/d'..b'44\\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \\"GET /api/jobs/fa6d20d0fb68383f HTTP/1.1\\" 200 None\\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \\"GET /api/histories/54f2a3a23292eb07/contents HTTP/1.1\\" 200 None\\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \\"GET /api/histories/54f2a3a23292eb07/contents/683bc220e21425bb HTTP/1.1\\" 200 None\\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \\"GET /api/histories/54f2a3a23292eb07/contents/683bc220e21425bb/provenance HTTP/1.1\\" 200 None\\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \\"GET /api/histories/54f2a3a23292eb07/contents/dataset_collections/2891970512fa2d5a HTTP/1.1\\" 200 None\\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \\"GET /api/histories/54f2a3a23292eb07/contents/a90a30fafe298e1e HTTP/1.1\\" 200 None\\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \\"GET /api/histories/54f2a3a23292eb07/contents/a90a30fafe298e1e/provenance HTTP/1.1\\" 200 None\\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \\"GET /api/jobs?history_id=54f2a3a23292eb07 HTTP/1.1\\" 200 None\\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \\"GET /api/jobs/fa6d20d0fb68383f?full=true HTTP/1.1\\" 200 None\\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \\"GET /api/jobs/fa6d20d0fb68383f HTTP/1.1\\" 200 None\\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \\"GET /api/histories/54f2a3a23292eb07/contents HTTP/1.1\\" 200 None\\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \\"GET /api/histories/54f2a3a23292eb07/contents/683bc220e21425bb HTTP/1.1\\" 200 None\\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \\"GET /api/histories/54f2a3a23292eb07/contents/683bc220e21425bb/provenance HTTP/1.1\\" 200 None\\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \\"GET /api/histories/54f2a3a23292eb07/contents/dataset_collections/2891970512fa2d5a HTTP/1.1\\" 200 None\\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \\"GET /api/histories/54f2a3a23292eb07/contents/a90a30fafe298e1e HTTP/1.1\\" 200 None\\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \\"GET /api/histories/54f2a3a23292eb07/contents/a90a30fafe298e1e/provenance HTTP/1.1\\" 200 None\\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \\"GET /api/jobs?history_id=54f2a3a23292eb07 HTTP/1.1\\" 200 None\\nurllib3.connectionpool: DEBUG: Starting new HTTP connection (1): 127.0.0.1:9844\\nurllib3.connectionpool: DEBUG: http://127.0.0.1:9844 \\"GET /api/dataset_collections/2891970512fa2d5a?instance_type=history HTTP/1.1\\" 200 None\\n--------------------- >> end captured logging << ---------------------"}}], "summary": {"num_tests": 3, "num_failures": 2, "num_errors": 0, "num_skips": 0}, "exit_code": 1}\n\\ No newline at end of file\n' |
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| diff -r 974bb00b2f43 -r acc4732fae0b test-data/krumsiek11_ranked_gene_groups.h5ad |
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| Binary file test-data/krumsiek11_ranked_gene_groups.h5ad has changed |
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| diff -r 974bb00b2f43 -r acc4732fae0b test-data/test.h5ad |
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| Binary file test-data/test.h5ad has changed |