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planemo upload for repository https://github.com/brsynth commit d8cc8b87fdb0374745b5420f2da7f08ae905c222-dirty
author tduigou
date Wed, 16 Jul 2025 14:28:21 +0000
parents 1a766d8d3883
children
comparison
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0:1a766d8d3883 1:34135dac85b0
7 }, 7 },
8 "tests": [ 8 "tests": [
9 { 9 {
10 "data": { 10 "data": {
11 "inputs": { 11 "inputs": {
12 "distribute_json": false, 12 "annotation_column": "annotation",
13 "json_from_workflow": [ 13 "avoid_patterns": "BsaI_site BsmBI_site BbsI_site SapI_site 8x1mer 5x3mer 9x2mer",
14 { 14 "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
15 "id": "051ed7ff50845d8c", 15 "execution": true,
16 "src": "hda" 16 "fragment_column": "fragment",
17 }, 17 "gc_constraints": "mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100",
18 { 18 "hairpin_constraints": "stem_size=20, hairpin_window=200",
19 "id": "25656ddfec77a3b3", 19 "kmer_size": "15",
20 "src": "hda" 20 "sequence_column": "sequence",
21 } 21 "table_name": "sample"
22 ]
23 }, 22 },
24 "job": { 23 "job": {
25 "command_line": "python '/home/rkhaled/galaxytools/tools/parameters_maystro/maystro.py' --distribute_json 'false' --json_from_workflow \"/tmp/tmpfpd6tei1/files/2/f/4/dataset_2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6.dat\" \"/tmp/tmpfpd6tei1/files/9/6/0/dataset_960eac8e-fb66-4982-8009-4896c9e57b38.dat\" --json_from_user 'None' --json_name_mapping /tmp/tmpfpd6tei1/files/2/f/4/dataset_2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6.dat:seq_from_db_param.json,/tmp/tmpfpd6tei1/files/9/6/0/dataset_960eac8e-fb66-4982-8009-4896c9e57b38.dat:seq_to_db_param.json --output_workflow '/tmp/tmpfpd6tei1/job_working_directory/000/3/outputs/dataset_d100f4ee-f845-4a68-be68-004c7af9679d.dat' --output_user '/tmp/tmpfpd6tei1/job_working_directory/000/3/outputs/dataset_1e2a9024-ad29-4d18-b95d-645817393383.dat' && echo 'DEBUB' && cat '/tmp/tmpfpd6tei1/job_working_directory/000/3/outputs/dataset_1e2a9024-ad29-4d18-b95d-645817393383.dat'", 24 "command_line": "python3 -c \"import json; params = { 'avoid_patterns': 'BsaI_site BsmBI_site BbsI_site SapI_site 8x1mer 5x3mer 9x2mer', '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', '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/tmpojrs64js/job_working_directory/000/1/outputs/dataset_ba54b8e6-58da-4f46-ab17-8f0c4d46bb3c.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBG && cat '/tmp/tmpojrs64js/job_working_directory/000/1/outputs/dataset_ba54b8e6-58da-4f46-ab17-8f0c4d46bb3c.dat' && echo DEBG && cat '/tmp/tmpojrs64js/job_working_directory/000/1/outputs/dataset_ba54b8e6-58da-4f46-ab17-8f0c4d46bb3c.dat'",
26 "command_version": "", 25 "command_version": "",
27 "copied_from_job_id": null, 26 "copied_from_job_id": null,
28 "create_time": "2025-07-11T09:42:39.854743", 27 "create_time": "2025-07-16T14:25:13.835798",
29 "dependencies": [], 28 "dependencies": [],
30 "exit_code": 0, 29 "exit_code": 0,
31 "external_id": "79277", 30 "external_id": "153937",
32 "galaxy_version": "25.0", 31 "galaxy_version": "25.0",
33 "handler": null, 32 "handler": null,
34 "history_id": "051ed7ff50845d8c", 33 "history_id": "479ca6463d0132e0",
35 "id": "d66447d427a79ce4", 34 "id": "479ca6463d0132e0",
35 "inputs": {},
36 "job_messages": [],
37 "job_metrics": [],
38 "job_runner_name": null,
39 "job_stderr": "",
40 "job_stdout": "",
41 "model_class": "Job",
42 "output_collections": {},
43 "outputs": {
44 "output_json": {
45 "id": "479ca6463d0132e0",
46 "src": "hda",
47 "uuid": "ba54b8e6-58da-4f46-ab17-8f0c4d46bb3c"
48 }
49 },
50 "params": {
51 "__input_ext": "\"input\"",
52 "annotation_column": "\"annotation\"",
53 "avoid_patterns": "\"BsaI_site BsmBI_site BbsI_site SapI_site 8x1mer 5x3mer 9x2mer\"",
54 "chromInfo": "\"/tmp/tmpojrs64js/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
55 "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"",
56 "dbkey": "\"?\"",
57 "execution": "true",
58 "fragment_column": "\"fragment\"",
59 "gc_constraints": "\"mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100\"",
60 "hairpin_constraints": "\"stem_size=20, hairpin_window=200\"",
61 "kmer_size": "\"15\"",
62 "sequence_column": "\"sequence\"",
63 "table_name": "\"sample\"",
64 "user_json": null
65 },
66 "state": "ok",
67 "stderr": "",
68 "stdout": "DEBG\n{\n \"avoid_patterns\": \"BsaI_site BsmBI_site BbsI_site SapI_site 8x1mer 5x3mer 9x2mer\",\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 \"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 \"avoid_patterns\": \"BsaI_site BsmBI_site BbsI_site SapI_site 8x1mer 5x3mer 9x2mer\",\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 \"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}",
69 "tool_id": "parameters_maystro",
70 "tool_stderr": "",
71 "tool_stdout": "DEBG\n{\n \"avoid_patterns\": \"BsaI_site BsmBI_site BbsI_site SapI_site 8x1mer 5x3mer 9x2mer\",\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 \"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 \"avoid_patterns\": \"BsaI_site BsmBI_site BbsI_site SapI_site 8x1mer 5x3mer 9x2mer\",\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 \"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}",
72 "update_time": "2025-07-16T14:25:27.820187",
73 "user_email": "planemo@galaxyproject.org",
74 "user_id": "479ca6463d0132e0"
75 },
76 "status": "success",
77 "test_index": 0,
78 "time_seconds": 14.118565320968628,
79 "tool_id": "parameters_maystro",
80 "tool_version": "1.1.0+galaxy3"
81 },
82 "has_data": true,
83 "id": "parameters_maystro-0"
84 },
85 {
86 "data": {
87 "inputs": {
88 "user_json": {
89 "id": "0311cb8bec9eec65",
90 "src": "hda"
91 }
92 },
93 "job": {
94 "command_line": "cp '/tmp/tmpojrs64js/files/a/6/4/dataset_a64b8b4b-290b-4b2e-bf77-d0d4ebc35137.dat' '/tmp/tmpojrs64js/job_working_directory/000/3/outputs/dataset_0dedeb7c-7969-452f-a162-25e70662b775.dat' && echo DEBG && cat '/tmp/tmpojrs64js/job_working_directory/000/3/outputs/dataset_0dedeb7c-7969-452f-a162-25e70662b775.dat'",
95 "command_version": "",
96 "copied_from_job_id": null,
97 "create_time": "2025-07-16T14:25:36.982208",
98 "dependencies": [],
99 "exit_code": 0,
100 "external_id": "154115",
101 "galaxy_version": "25.0",
102 "handler": null,
103 "history_id": "0311cb8bec9eec65",
104 "id": "da029efde06939a6",
36 "inputs": { 105 "inputs": {
37 "json_from_workflow": { 106 "user_json": {
38 "id": "051ed7ff50845d8c", 107 "id": "0311cb8bec9eec65",
39 "src": "hda", 108 "src": "hda",
40 "uuid": "2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6" 109 "uuid": "a64b8b4b-290b-4b2e-bf77-d0d4ebc35137"
41 },
42 "json_from_workflow1": {
43 "id": "051ed7ff50845d8c",
44 "src": "hda",
45 "uuid": "2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6"
46 },
47 "json_from_workflow2": {
48 "id": "25656ddfec77a3b3",
49 "src": "hda",
50 "uuid": "960eac8e-fb66-4982-8009-4896c9e57b38"
51 } 110 }
52 }, 111 },
53 "job_messages": [], 112 "job_messages": [],
54 "job_metrics": [], 113 "job_metrics": [],
55 "job_runner_name": null, 114 "job_runner_name": null,
56 "job_stderr": "", 115 "job_stderr": "",
57 "job_stdout": "", 116 "job_stdout": "",
58 "model_class": "Job", 117 "model_class": "Job",
59 "output_collections": {}, 118 "output_collections": {},
60 "outputs": { 119 "outputs": {
61 "output_user": { 120 "output_json": {
62 "id": "39496c7f8d685f43", 121 "id": "da029efde06939a6",
63 "src": "hda", 122 "src": "hda",
64 "uuid": "1e2a9024-ad29-4d18-b95d-645817393383" 123 "uuid": "0dedeb7c-7969-452f-a162-25e70662b775"
65 },
66 "output_workflow": {
67 "id": "d66447d427a79ce4",
68 "src": "hda",
69 "uuid": "d100f4ee-f845-4a68-be68-004c7af9679d"
70 } 124 }
71 }, 125 },
72 "params": { 126 "params": {
73 "__input_ext": "\"input\"", 127 "__input_ext": "\"input\"",
74 "chromInfo": "\"/tmp/tmpfpd6tei1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 128 "annotation_column": null,
129 "avoid_patterns": null,
130 "chromInfo": "\"/tmp/tmpojrs64js/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
131 "db_uri": null,
75 "dbkey": "\"?\"", 132 "dbkey": "\"?\"",
76 "distribute_json": "false", 133 "execution": "false",
77 "json_from_user": null 134 "fragment_column": null,
135 "gc_constraints": null,
136 "hairpin_constraints": null,
137 "kmer_size": "\"\"",
138 "sequence_column": null,
139 "table_name": null
78 }, 140 },
79 "state": "ok", 141 "state": "ok",
80 "stderr": "", 142 "stderr": "",
81 "stdout": "[INFO] Watching temp dir for new JSONs: /tmp/tmpfpd6tei1/tmp/maystro_merge_xd06s1et\n[INFO] Initial JSONs from workflow: ['/tmp/tmpfpd6tei1/files/2/f/4/dataset_2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6.dat', '/tmp/tmpfpd6tei1/files/9/6/0/dataset_960eac8e-fb66-4982-8009-4896c9e57b38.dat']\n[INFO] Added data under key: seq_from_db_param\n[INFO] Added data under key: seq_to_db_param\n[INFO] Merged JSON written to: /tmp/tmpfpd6tei1/job_working_directory/000/3/outputs/dataset_1e2a9024-ad29-4d18-b95d-645817393383.dat\n[INFO] Cleaning up: /tmp/tmpfpd6tei1/tmp/maystro_merge_xd06s1et\nDEBUB\n{\n \"seq_from_db_param\": {\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 \"seq_to_db_param\": {\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}", 143 "stdout": "DEBG\n{\n \"avoid_patterns\": \"BsaI_site\\nBsmBI_site\\nBbsI_site\\nSapI_site\\n8x1mer\\n5x3mer\\n9x2mer\",\n \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100\\nmini=0.1, maxi=0.9, window=100\",\n \"kmer_size\": \"15\",\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",
82 "tool_id": "parameters_maystro", 144 "tool_id": "parameters_maystro",
83 "tool_stderr": "", 145 "tool_stderr": "",
84 "tool_stdout": "[INFO] Watching temp dir for new JSONs: /tmp/tmpfpd6tei1/tmp/maystro_merge_xd06s1et\n[INFO] Initial JSONs from workflow: ['/tmp/tmpfpd6tei1/files/2/f/4/dataset_2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6.dat', '/tmp/tmpfpd6tei1/files/9/6/0/dataset_960eac8e-fb66-4982-8009-4896c9e57b38.dat']\n[INFO] Added data under key: seq_from_db_param\n[INFO] Added data under key: seq_to_db_param\n[INFO] Merged JSON written to: /tmp/tmpfpd6tei1/job_working_directory/000/3/outputs/dataset_1e2a9024-ad29-4d18-b95d-645817393383.dat\n[INFO] Cleaning up: /tmp/tmpfpd6tei1/tmp/maystro_merge_xd06s1et\nDEBUB\n{\n \"seq_from_db_param\": {\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 \"seq_to_db_param\": {\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}", 146 "tool_stdout": "DEBG\n{\n \"avoid_patterns\": \"BsaI_site\\nBsmBI_site\\nBbsI_site\\nSapI_site\\n8x1mer\\n5x3mer\\n9x2mer\",\n \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100\\nmini=0.1, maxi=0.9, window=100\",\n \"kmer_size\": \"15\",\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",
85 "update_time": "2025-07-11T09:42:45.494563", 147 "update_time": "2025-07-16T14:25:42.101497",
86 "user_email": "planemo@galaxyproject.org", 148 "user_email": "planemo@galaxyproject.org",
87 "user_id": "051ed7ff50845d8c" 149 "user_id": "479ca6463d0132e0"
88 },
89 "status": "success",
90 "test_index": 0,
91 "time_seconds": 16.301273107528687,
92 "tool_id": "parameters_maystro",
93 "tool_version": "0.1.0+galaxy1"
94 },
95 "has_data": true,
96 "id": "parameters_maystro-0"
97 },
98 {
99 "data": {
100 "inputs": {
101 "distribute_json": true,
102 "json_from_user": {
103 "id": "10ea9be91661a5fd",
104 "src": "hda"
105 },
106 "json_from_workflow": [
107 {
108 "id": "b7e19a053756efb9",
109 "src": "hda"
110 },
111 {
112 "id": "45e8a4dfb17d83f9",
113 "src": "hda"
114 }
115 ]
116 },
117 "job": {
118 "command_line": "python '/home/rkhaled/galaxytools/tools/parameters_maystro/maystro.py' --distribute_json 'true' --json_from_workflow \"/tmp/tmpfpd6tei1/files/c/1/e/dataset_c1e98b32-965c-4a0d-9c7f-26973a7e0fe6.dat\" \"/tmp/tmpfpd6tei1/files/3/a/5/dataset_3a560c20-0d3f-4aae-abd4-4a460698f28f.dat\" --json_from_user '/tmp/tmpfpd6tei1/files/0/a/b/dataset_0abf65a6-bd5b-47fc-94ba-a6a97fa6d88b.dat' --json_name_mapping /tmp/tmpfpd6tei1/files/c/1/e/dataset_c1e98b32-965c-4a0d-9c7f-26973a7e0fe6.dat:seq_from_db_param.json,/tmp/tmpfpd6tei1/files/3/a/5/dataset_3a560c20-0d3f-4aae-abd4-4a460698f28f.dat:seq_to_db_param.json --output_workflow '/tmp/tmpfpd6tei1/job_working_directory/000/7/outputs/dataset_5254084b-4d71-4098-b933-f73a9e7d5a28.dat' --output_user '/tmp/tmpfpd6tei1/job_working_directory/000/7/outputs/dataset_04c60445-2ff4-4b59-bcbc-75f08b68625a.dat' && echo 'DEBUB' && cat '/tmp/tmpfpd6tei1/job_working_directory/000/7/outputs/dataset_04c60445-2ff4-4b59-bcbc-75f08b68625a.dat'",
119 "command_version": "",
120 "copied_from_job_id": null,
121 "create_time": "2025-07-11T09:42:56.883885",
122 "dependencies": [],
123 "exit_code": 0,
124 "external_id": "79598",
125 "galaxy_version": "25.0",
126 "handler": null,
127 "history_id": "25656ddfec77a3b3",
128 "id": "10ea9be91661a5fd",
129 "inputs": {
130 "json_from_user": {
131 "id": "10ea9be91661a5fd",
132 "src": "hda",
133 "uuid": "0abf65a6-bd5b-47fc-94ba-a6a97fa6d88b"
134 },
135 "json_from_workflow": {
136 "id": "b7e19a053756efb9",
137 "src": "hda",
138 "uuid": "c1e98b32-965c-4a0d-9c7f-26973a7e0fe6"
139 },
140 "json_from_workflow1": {
141 "id": "b7e19a053756efb9",
142 "src": "hda",
143 "uuid": "c1e98b32-965c-4a0d-9c7f-26973a7e0fe6"
144 },
145 "json_from_workflow2": {
146 "id": "45e8a4dfb17d83f9",
147 "src": "hda",
148 "uuid": "3a560c20-0d3f-4aae-abd4-4a460698f28f"
149 }
150 },
151 "job_messages": [],
152 "job_metrics": [],
153 "job_runner_name": null,
154 "job_stderr": "",
155 "job_stdout": "",
156 "model_class": "Job",
157 "output_collections": {},
158 "outputs": {
159 "output_user": {
160 "id": "295d652904818249",
161 "src": "hda",
162 "uuid": "04c60445-2ff4-4b59-bcbc-75f08b68625a"
163 },
164 "output_workflow": {
165 "id": "8c61ed432685cfe0",
166 "src": "hda",
167 "uuid": "5254084b-4d71-4098-b933-f73a9e7d5a28"
168 }
169 },
170 "params": {
171 "__input_ext": "\"input\"",
172 "chromInfo": "\"/tmp/tmpfpd6tei1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
173 "dbkey": "\"?\"",
174 "distribute_json": "true"
175 },
176 "state": "ok",
177 "stderr": "",
178 "stdout": "DEBUB\n",
179 "tool_id": "parameters_maystro",
180 "tool_stderr": "",
181 "tool_stdout": "DEBUB\n",
182 "update_time": "2025-07-11T09:43:02.149865",
183 "user_email": "planemo@galaxyproject.org",
184 "user_id": "051ed7ff50845d8c"
185 }, 150 },
186 "status": "success", 151 "status": "success",
187 "test_index": 1, 152 "test_index": 1,
188 "time_seconds": 16.54760479927063, 153 "time_seconds": 14.252628803253174,
189 "tool_id": "parameters_maystro", 154 "tool_id": "parameters_maystro",
190 "tool_version": "0.1.0+galaxy1" 155 "tool_version": "1.1.0+galaxy3"
191 }, 156 },
192 "has_data": true, 157 "has_data": true,
193 "id": "parameters_maystro-1" 158 "id": "parameters_maystro-1"
194 } 159 }
195 ], 160 ],