# HG changeset patch
# User tduigou
# Date 1743600561 0
# Node ID 3449d7bfee20f04f8aa3904fe6e01e862b85069f
# Parent c320aba02826a94dc5dacc9292e87ec373efa939
planemo upload for repository https://github.com/brsynth/rrparser commit 65769d2b12a952ffbe74c2cd61e47af873829d1a
diff -r c320aba02826 -r 3449d7bfee20 output.html
--- a/output.html Wed Apr 02 13:24:04 2025 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,291 +0,0 @@
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diff -r c320aba02826 -r 3449d7bfee20 output.json
--- a/output.json Wed Apr 02 13:24:04 2025 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,545 +0,0 @@
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- "chromInfo": "\"/tmp/tmpm3epclar/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
- "dbkey": "\"?\"",
- "rules": "{\"__current_case__\": 3, \"file\": {\"values\": [{\"id\": 8, \"src\": \"hda\"}]}, \"input_format\": \"csv\", \"type\": \"rules-file\"}"
- },
- "state": "ok",
- "stderr": "\u001b[32m\nrrparser 2.6.0\n\u001b[0m\n\u001b[32mFiltering rules:\u001b[0m\n\u001b[32m -> EC numbers (not in): ['1.1.1.202', '2.3.1.40', 'NOEC', '1.2.3', '2.4.1\\n']\u001b[0m\n\u001b[32m -> Diameters: [2, 4, 6, 8, 10, 12, 14, 16]\u001b[0m\n\u001b[32m -> Rule types: all\u001b[0m\n\u001b[32m\u001b[0m\n\u001b[32m=> 68 rules found\u001b[0m\n\u001b[32m\u001b[0m\n\u001b[32mWriting results...\u001b[0m\n",
- "stdout": "",
- "tool_id": "rrparser",
- "tool_stderr": "\u001b[32m\nrrparser 2.6.0\n\u001b[0m\n\u001b[32mFiltering rules:\u001b[0m\n\u001b[32m -> EC numbers (not in): ['1.1.1.202', '2.3.1.40', 'NOEC', '1.2.3', '2.4.1\\n']\u001b[0m\n\u001b[32m -> Diameters: [2, 4, 6, 8, 10, 12, 14, 16]\u001b[0m\n\u001b[32m -> Rule types: all\u001b[0m\n\u001b[32m\u001b[0m\n\u001b[32m=> 68 rules found\u001b[0m\n\u001b[32m\u001b[0m\n\u001b[32mWriting results...\u001b[0m\n",
- "tool_stdout": "",
- "update_time": "2025-04-02T13:19:58.249593",
- "user_email": "planemo@galaxyproject.org",
- "user_id": "9e4e5a4b3a855398"
- },
- "status": "success",
- "test_index": 4,
- "time_seconds": 17.527034759521484,
- "tool_id": "rrparser",
- "tool_version": "2.7.0+galaxy2"
- },
- "has_data": true,
- "id": "rrparser-4"
- },
- {
- "data": {
- "inputs": {
- "adv|input_scores_file": {
- "id": "e518de1807107326",
- "src": "hda"
- },
- "rules|file": {
- "id": "1ecde2b521ddcb43",
- "src": "hda"
- },
- "rules|type": "rules-file"
- },
- "job": {
- "command_line": "python -m rrparser --rules_file '/tmp/tmpm3epclar/files/9/c/c/dataset_9cc4cc4e-4aa9-4f11-ba74-f94f9ff8bd58.dat' --input-format 'csv' --diameters '2,4,6,8,10,12,14,16' --output-format csv --rules-dir \"${TMPDIR:-.}\" --outfile '/tmp/tmpm3epclar/job_working_directory/000/13/outputs/dataset_7b814b69-02aa-4a6a-87e9-df3c7506f8e0.dat' --scores '/tmp/tmpm3epclar/files/9/c/9/dataset_9c94b8d9-170b-42d3-be35-8ec09d2f651c.dat'",
- "command_version": "",
- "copied_from_job_id": null,
- "create_time": "2025-04-02T13:20:08.972566",
- "dependencies": [
- {
- "cacheable": false,
- "dependency_resolver": {
- "auto_init": true,
- "auto_install": true,
- "can_uninstall_dependencies": true,
- "ensure_channels": "conda-forge,bioconda",
- "model_class": "CondaDependencyResolver",
- "prefix": "/home/rkhaled/miniconda3",
- "read_only": false,
- "resolver_type": "conda",
- "resolves_simple_dependencies": true,
- "use_local": false,
- "versionless": false
- },
- "dependency_type": "conda",
- "environment_path": "/home/rkhaled/miniconda3/envs/__rrparser@2.7.0",
- "exact": true,
- "model_class": "MergedCondaDependency",
- "name": "rrparser",
- "version": "2.7.0"
- }
- ],
- "exit_code": 0,
- "external_id": "177372",
- "galaxy_version": "24.2",
- "handler": null,
- "history_id": "158df96eaa64fd08",
- "id": "bec2ef2bb04a8edc",
- "inputs": {
- "adv|input_scores_file": {
- "id": "e518de1807107326",
- "src": "hda",
- "uuid": "9c94b8d9-170b-42d3-be35-8ec09d2f651c"
- },
- "rules|file": {
- "id": "1ecde2b521ddcb43",
- "src": "hda",
- "uuid": "9cc4cc4e-4aa9-4f11-ba74-f94f9ff8bd58"
- }
- },
- "job_messages": [],
- "job_metrics": [],
- "job_runner_name": null,
- "job_stderr": "",
- "job_stdout": "",
- "model_class": "Job",
- "output_collections": {},
- "outputs": {
- "out_rules": {
- "id": "bec2ef2bb04a8edc",
- "src": "hda",
- "uuid": "7b814b69-02aa-4a6a-87e9-df3c7506f8e0"
- }
- },
- "params": {
- "__input_ext": "\"input\"",
- "adv": "{\"compress\": false, \"diameters\": [\"2\", \"4\", \"6\", \"8\", \"10\", \"12\", \"14\", \"16\"], \"input_conditional_ec\": {\"__current_case__\": 0, \"input_type\": \"no\"}, \"input_scores_file\": {\"values\": [{\"id\": 12, \"src\": \"hda\"}]}}",
- "chromInfo": "\"/tmp/tmpm3epclar/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
- "dbkey": "\"?\"",
- "rules": "{\"__current_case__\": 3, \"file\": {\"values\": [{\"id\": 11, \"src\": \"hda\"}]}, \"input_format\": \"csv\", \"type\": \"rules-file\"}"
- },
- "state": "ok",
- "stderr": "\u001b[32m\nrrparser 2.6.0\n\u001b[0m\n\u001b[32mFiltering rules:\u001b[0m\n\u001b[32m -> EC numbers (not in): []\u001b[0m\n\u001b[32m -> Diameters: [2, 4, 6, 8, 10, 12, 14, 16]\u001b[0m\n\u001b[32m -> Rule types: all\u001b[0m\n\u001b[32m\u001b[0m\n\u001b[32m=> 99 rules found\u001b[0m\n\u001b[32m\u001b[0m\n\u001b[33mRule IDs {'foo'} found in scores file but not in results. Its score will not be used.\u001b[0m\n\u001b[32mWriting results...\u001b[0m\n",
- "stdout": "",
- "tool_id": "rrparser",
- "tool_stderr": "\u001b[32m\nrrparser 2.6.0\n\u001b[0m\n\u001b[32mFiltering rules:\u001b[0m\n\u001b[32m -> EC numbers (not in): []\u001b[0m\n\u001b[32m -> Diameters: [2, 4, 6, 8, 10, 12, 14, 16]\u001b[0m\n\u001b[32m -> Rule types: all\u001b[0m\n\u001b[32m\u001b[0m\n\u001b[32m=> 99 rules found\u001b[0m\n\u001b[32m\u001b[0m\n\u001b[33mRule IDs {'foo'} found in scores file but not in results. Its score will not be used.\u001b[0m\n\u001b[32mWriting results...\u001b[0m\n",
- "tool_stdout": "",
- "update_time": "2025-04-02T13:20:15.699056",
- "user_email": "planemo@galaxyproject.org",
- "user_id": "9e4e5a4b3a855398"
- },
- "status": "success",
- "test_index": 5,
- "time_seconds": 17.1466064453125,
- "tool_id": "rrparser",
- "tool_version": "2.7.0+galaxy2"
- },
- "has_data": true,
- "id": "rrparser-5"
- }
- ],
- "version": "0.1"
-}
\ No newline at end of file
diff -r c320aba02826 -r 3449d7bfee20 rrparser.xml
--- a/rrparser.xml Wed Apr 02 13:24:04 2025 +0000
+++ b/rrparser.xml Wed Apr 02 13:29:21 2025 +0000
@@ -1,7 +1,7 @@
Retrieve the reaction rules from RetroRules
- 2
+ 3
2.7.0