Mercurial > repos > tduigou > parameters_maystro_workflow_0

comparison output.json @ 0:9ab8b3673816 draft default tip

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planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools/parameters_maystro commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
author tduigou
date Wed, 23 Jul 2025 09:39:39 +0000
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-1:000000000000 0:9ab8b3673816
1 {
2 "summary": {
3 "num_errors": 0,
4 "num_failures": 0,
5 "num_skips": 0,
6 "num_tests": 2
7 },
8 "tests": [
9 {
10 "data": {
11 "inputs": {
12 "DB|annotation_column": "annotation",
13 "DB|db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
14 "DB|execution": true,
15 "DB|fragment_column": "fragment",
16 "DB|sequence_column": "sequence",
17 "DB|table_name": "sample",
18 "DnaOptimizationProblemClass": "DnaOptimizationProblem",
19 "assembly_plan_name": "Type2sRestrictionAssembly",
20 "avoid_patterns": "BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer",
21 "enzyme": "auto",
22 "gc_constraints": "mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100",
23 "hairpin_constraints": "stem_size=20, hairpin_window=200",
24 "kmer_size": "15",
25 "methylation_protection": true,
26 "topology": "circular"
27 },
28 "job": {
29 "command_line": "python3 -c \"import json; params = { 'DnaOptimizationProblemClass': 'DnaOptimizationProblem', 'methylation_protection': 'true', 'allow_edits': 'true', 'avoid_patterns': 'BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer', 'hairpin_constraints': 'stem_size=20, hairpin_window=200', 'gc_constraints': 'mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100', 'kmer_size': '15', 'assembly_plan_name': 'Type2sRestrictionAssembly', 'topology': 'circular', 'enzyme': 'auto', 'execution': 'true', 'db_uri': 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db', 'table': 'sample', 'fragment_column': 'fragment', 'sequence_column': 'sequence', 'annotation_column': 'annotation' }; f = open('/tmp/tmpnxavcgf5/job_working_directory/000/1/outputs/dataset_53ffa695-5fab-48b3-b5f5-ff93f77bfc10.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBG && cat '/tmp/tmpnxavcgf5/job_working_directory/000/1/outputs/dataset_53ffa695-5fab-48b3-b5f5-ff93f77bfc10.dat' && echo DEBG && cat '/tmp/tmpnxavcgf5/job_working_directory/000/1/outputs/dataset_53ffa695-5fab-48b3-b5f5-ff93f77bfc10.dat'",
30 "command_version": "",
31 "copied_from_job_id": null,
32 "create_time": "2025-07-17T12:08:28.832103",
33 "dependencies": [],
34 "exit_code": 0,
35 "external_id": "135810",
36 "galaxy_version": "25.0",
37 "handler": null,
38 "history_id": "d952758136b0c83c",
39 "id": "d952758136b0c83c",
40 "inputs": {},
41 "job_messages": [],
42 "job_metrics": [],
43 "job_runner_name": null,
44 "job_stderr": "",
45 "job_stdout": "",
46 "model_class": "Job",
47 "output_collections": {},
48 "outputs": {
49 "output_json": {
50 "id": "d952758136b0c83c",
51 "src": "hda",
52 "uuid": "53ffa695-5fab-48b3-b5f5-ff93f77bfc10"
53 }
54 },
55 "params": {
56 "DB": "{\"annotation_column\": \"annotation\", \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\", \"execution\": true, \"fragment_column\": \"fragment\", \"sequence_column\": \"sequence\", \"table_name\": \"sample\", \"user_json\": null}",
57 "DnaOptimizationProblemClass": "\"DnaOptimizationProblem\"",
58 "__input_ext": "\"input\"",
59 "allow_edits": "true",
60 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
61 "avoid_patterns": "\"BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer\"",
62 "chromInfo": "\"/tmp/tmpnxavcgf5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
63 "dbkey": "\"?\"",
64 "enzyme": "\"auto\"",
65 "gc_constraints": "\"mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100\"",
66 "hairpin_constraints": "\"stem_size=20, hairpin_window=200\"",
67 "kmer_size": "\"15\"",
68 "methylation_protection": "true",
69 "topology": "\"circular\""
70 },
71 "state": "ok",
72 "stderr": "",
73 "stdout": "DEBG\n{\n \"DnaOptimizationProblemClass\": \"DnaOptimizationProblem\",\n \"methylation_protection\": \"true\",\n \"allow_edits\": \"true\",\n \"avoid_patterns\": \"BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer\",\n \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100\",\n \"kmer_size\": \"15\",\n \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\",\n \"execution\": \"true\",\n \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n}DEBG\n{\n \"DnaOptimizationProblemClass\": \"DnaOptimizationProblem\",\n \"methylation_protection\": \"true\",\n \"allow_edits\": \"true\",\n \"avoid_patterns\": \"BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer\",\n \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100\",\n \"kmer_size\": \"15\",\n \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\",\n \"execution\": \"true\",\n \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n}",
74 "tool_id": "parameters_maystro_workflow_2",
75 "tool_stderr": "",
76 "tool_stdout": "DEBG\n{\n \"DnaOptimizationProblemClass\": \"DnaOptimizationProblem\",\n \"methylation_protection\": \"true\",\n \"allow_edits\": \"true\",\n \"avoid_patterns\": \"BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer\",\n \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100\",\n \"kmer_size\": \"15\",\n \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\",\n \"execution\": \"true\",\n \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n}DEBG\n{\n \"DnaOptimizationProblemClass\": \"DnaOptimizationProblem\",\n \"methylation_protection\": \"true\",\n \"allow_edits\": \"true\",\n \"avoid_patterns\": \"BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer\",\n \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100\",\n \"kmer_size\": \"15\",\n \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\",\n \"execution\": \"true\",\n \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n}",
77 "update_time": "2025-07-17T12:08:33.771569",
78 "user_email": "planemo@galaxyproject.org",
79 "user_id": "d952758136b0c83c"
80 },
81 "status": "success",
82 "test_index": 0,
83 "time_seconds": 5.093859434127808,
84 "tool_id": "parameters_maystro_workflow_2",
85 "tool_version": "0.1.0"
86 },
87 "has_data": true,
88 "id": "parameters_maystro_workflow_2-0"
89 },
90 {
91 "data": {
92 "inputs": {
93 "DB|user_json": {
94 "id": "b08444d846605ee4",
95 "src": "hda"
96 }
97 },
98 "job": {
99 "command_line": "cp '/tmp/tmpnxavcgf5/files/b/b/d/dataset_bbd9a440-a787-439e-9b36-2c1c45dae0a3.dat' '/tmp/tmpnxavcgf5/job_working_directory/000/3/outputs/dataset_6eed7c7c-77ce-4d77-b2ef-0a367df7e250.dat' && echo DEBG && cat '/tmp/tmpnxavcgf5/job_working_directory/000/3/outputs/dataset_6eed7c7c-77ce-4d77-b2ef-0a367df7e250.dat'",
100 "command_version": "",
101 "copied_from_job_id": null,
102 "create_time": "2025-07-17T12:08:43.857384",
103 "dependencies": [],
104 "exit_code": 0,
105 "external_id": "135995",
106 "galaxy_version": "25.0",
107 "handler": null,
108 "history_id": "b08444d846605ee4",
109 "id": "e67c2cbedbcb0da1",
110 "inputs": {
111 "DB|user_json": {
112 "id": "b08444d846605ee4",
113 "src": "hda",
114 "uuid": "bbd9a440-a787-439e-9b36-2c1c45dae0a3"
115 }
116 },
117 "job_messages": [],
118 "job_metrics": [],
119 "job_runner_name": null,
120 "job_stderr": "",
121 "job_stdout": "",
122 "model_class": "Job",
123 "output_collections": {},
124 "outputs": {
125 "output_json": {
126 "id": "e67c2cbedbcb0da1",
127 "src": "hda",
128 "uuid": "6eed7c7c-77ce-4d77-b2ef-0a367df7e250"
129 }
130 },
131 "params": {
132 "DB": "{\"annotation_column\": null, \"db_uri\": null, \"execution\": false, \"fragment_column\": null, \"sequence_column\": null, \"table_name\": null, \"user_json\": {\"values\": [{\"id\": 2, \"src\": \"hda\"}]}}",
133 "DnaOptimizationProblemClass": "\"DnaOptimizationProblem\"",
134 "__input_ext": "\"input\"",
135 "allow_edits": "true",
136 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
137 "avoid_patterns": null,
138 "chromInfo": "\"/tmp/tmpnxavcgf5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
139 "dbkey": "\"?\"",
140 "enzyme": "\"auto\"",
141 "gc_constraints": null,
142 "hairpin_constraints": null,
143 "kmer_size": "\"\"",
144 "methylation_protection": "false",
145 "topology": "\"circular\""
146 },
147 "state": "ok",
148 "stderr": "",
149 "stdout": "DEBG\n{\n \"DnaOptimizationProblemClass\":\"DnaOptimizationProblem\",\n \"avoid_patterns\": \"BsaI_site\\nNotI_site\\nXbaI_site\\nClaI_site\\n8x1mer\",\n \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\\nstem_size=10, hairpin_window=100\",\n \"gc_constraints\": \"mini=0.1, maxi=0.9\\nmini-0.3, maxi=0.7, window=50\",\n \"kmer_size\": \"15\",\n \"methylation_protection\":\"methylation_protection\",\n \"allow_edits\":\"True\",\n \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\",\n \"execution\": \"true\",\n \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n}\n",
150 "tool_id": "parameters_maystro_workflow_2",
151 "tool_stderr": "",
152 "tool_stdout": "DEBG\n{\n \"DnaOptimizationProblemClass\":\"DnaOptimizationProblem\",\n \"avoid_patterns\": \"BsaI_site\\nNotI_site\\nXbaI_site\\nClaI_site\\n8x1mer\",\n \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\\nstem_size=10, hairpin_window=100\",\n \"gc_constraints\": \"mini=0.1, maxi=0.9\\nmini-0.3, maxi=0.7, window=50\",\n \"kmer_size\": \"15\",\n \"methylation_protection\":\"methylation_protection\",\n \"allow_edits\":\"True\",\n \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\",\n \"execution\": \"true\",\n \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n}\n",
153 "update_time": "2025-07-17T12:08:49.096516",
154 "user_email": "planemo@galaxyproject.org",
155 "user_id": "d952758136b0c83c"
156 },
157 "status": "success",
158 "test_index": 1,
159 "time_seconds": 15.298557996749878,
160 "tool_id": "parameters_maystro_workflow_2",
161 "tool_version": "0.1.0"
162 },
163 "has_data": true,
164 "id": "parameters_maystro_workflow_2-1"
165 }
166 ],
167 "version": "0.1"
168 }