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comparison output.json @ 1:bf8cd9487e33 draft

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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Tue, 13 May 2025 07:22:36 +0000
parents 8fd9af4cb080
children f78651af72e4
comparison
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0:8fd9af4cb080 1:bf8cd9487e33
10 "data": { 10 "data": {
11 "inputs": { 11 "inputs": {
12 "adv|allow_edits": true, 12 "adv|allow_edits": true,
13 "adv|use_file_names_as_ids": true, 13 "adv|use_file_names_as_ids": true,
14 "domestication_csv": { 14 "domestication_csv": {
15 "id": "aaa883914c50d913", 15 "id": "6c832fb8ac42860f",
16 "src": "hda" 16 "src": "hda"
17 }, 17 },
18 "genbank_files": [ 18 "genbank_files": {
19 { 19 "id": "e660c01bdba47572",
20 "id": "f16125b2a7e364b6", 20 "src": "hdca"
21 "src": "hda" 21 },
22 },
23 {
24 "id": "723c01d174904c31",
25 "src": "hda"
26 },
27 {
28 "id": "6f9854c84e6fb32c",
29 "src": "hda"
30 },
31 {
32 "id": "ac6038717ee9c106",
33 "src": "hda"
34 },
35 {
36 "id": "1b3b4b31ea959cca",
37 "src": "hda"
38 },
39 {
40 "id": "7144c3d02f40c0d6",
41 "src": "hda"
42 },
43 {
44 "id": "9d14f67ce73d06b8",
45 "src": "hda"
46 }
47 ],
48 "methylation_protection": false 22 "methylation_protection": false
49 }, 23 },
50 "job": { 24 "job": {
51 "command_line": "mkdir 'outdir_gb' && mkdir 'outdir_zip' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpbjg5_060/files/1/7/7/dataset_1773336e-37c8-467a-932e-47c5d4bc7247.dat,/tmp/tmpbjg5_060/files/e/e/4/dataset_ee4defe5-2762-48fb-b10b-350bfbb4b71d.dat,/tmp/tmpbjg5_060/files/4/0/4/dataset_4041b0a0-86b9-4a81-9e95-77031b1fb96f.dat,/tmp/tmpbjg5_060/files/f/a/8/dataset_fa8e14e1-6c87-4a13-801f-ecb72b5e9517.dat,/tmp/tmpbjg5_060/files/0/7/b/dataset_07b8841b-22ef-4142-8931-7ae4111f1887.dat,/tmp/tmpbjg5_060/files/a/6/5/dataset_a653f705-9192-485d-94f3-22b66714c9fb.dat,/tmp/tmpbjg5_060/files/1/e/a/dataset_1ea79cfa-b478-4c9b-b906-9b08526c85f4.dat' --csv_file '/tmp/tmpbjg5_060/files/8/d/0/dataset_8d08fc90-ab45-4d65-8912-1edef99b50e5.dat' --file_name_mapping '/tmp/tmpbjg5_060/files/1/7/7/dataset_1773336e-37c8-467a-932e-47c5d4bc7247.dat:p3_2_CAG.gb,/tmp/tmpbjg5_060/files/e/e/4/dataset_ee4defe5-2762-48fb-b10b-350bfbb4b71d.dat:p7_gfp_sequence.gb,/tmp/tmpbjg5_060/files/4/0/4/dataset_4041b0a0-86b9-4a81-9e95-77031b1fb96f.dat:p14_CMVp.gb,/tmp/tmpbjg5_060/files/f/a/8/dataset_fa8e14e1-6c87-4a13-801f-ecb72b5e9517.dat:p16_bGHpolyA.gb,/tmp/tmpbjg5_060/files/0/7/b/dataset_07b8841b-22ef-4142-8931-7ae4111f1887.dat:p18_CMVp.gb,/tmp/tmpbjg5_060/files/a/6/5/dataset_a653f705-9192-485d-94f3-22b66714c9fb.dat:p19_mNeoGreen.gb,/tmp/tmpbjg5_060/files/1/e/a/dataset_1ea79cfa-b478-4c9b-b906-9b08526c85f4.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_methprot 'outdir_gb' --methylation_protection 'false' && cp 'output_zip.zip' '/tmp/tmpbjg5_060/job_working_directory/000/9/outputs/dataset_3bd2c885-c568-4c63-8f50-4d3f470c77a5.dat'", 25 "command_line": "mkdir 'outdir_gb' && mkdir 'outdir_zip' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpmomj1390/files/9/8/e/dataset_98eaff26-0334-4311-b121-579c564457fa.dat,/tmp/tmpmomj1390/files/6/9/e/dataset_69e06834-aff3-45c0-8c8a-1b0951b3c58a.dat,/tmp/tmpmomj1390/files/a/4/3/dataset_a43d91b4-75bc-42ad-b3eb-3c2b8974849d.dat,/tmp/tmpmomj1390/files/b/8/4/dataset_b8425ed5-d152-443a-ab5e-d5e5d8e18685.dat,/tmp/tmpmomj1390/files/a/f/5/dataset_af5ff6ae-e7f3-4d04-9e27-2f4619b9a7f5.dat,/tmp/tmpmomj1390/files/d/f/b/dataset_dfbae617-1607-410e-ae63-95e367876898.dat,/tmp/tmpmomj1390/files/9/9/d/dataset_99d37e87-dd8a-4439-a03a-004433442d3f.dat' --csv_file '/tmp/tmpmomj1390/files/f/b/c/dataset_fbc30e96-b97e-4267-8ed5-5ceaa219759e.dat' --file_name_mapping '/tmp/tmpmomj1390/files/9/8/e/dataset_98eaff26-0334-4311-b121-579c564457fa.dat:p3_2_CAG.gb,/tmp/tmpmomj1390/files/6/9/e/dataset_69e06834-aff3-45c0-8c8a-1b0951b3c58a.dat:p7_gfp_sequence.gb,/tmp/tmpmomj1390/files/a/4/3/dataset_a43d91b4-75bc-42ad-b3eb-3c2b8974849d.dat:p14_CMVp.gb,/tmp/tmpmomj1390/files/b/8/4/dataset_b8425ed5-d152-443a-ab5e-d5e5d8e18685.dat:p16_bGHpolyA.gb,/tmp/tmpmomj1390/files/a/f/5/dataset_af5ff6ae-e7f3-4d04-9e27-2f4619b9a7f5.dat:p18_CMVp.gb,/tmp/tmpmomj1390/files/d/f/b/dataset_dfbae617-1607-410e-ae63-95e367876898.dat:p19_mNeoGreen.gb,/tmp/tmpmomj1390/files/9/9/d/dataset_99d37e87-dd8a-4439-a03a-004433442d3f.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_methprot 'outdir_gb' --methylation_protection 'false' && cp 'output_zip.zip' '/tmp/tmpmomj1390/job_working_directory/000/9/outputs/dataset_6e663eda-900f-4c38-aa98-8ed6be291879.dat'",
52 "command_version": "", 26 "command_version": "",
53 "copied_from_job_id": null, 27 "copied_from_job_id": null,
54 "create_time": "2025-05-12T10:19:22.845477", 28 "create_time": "2025-05-12T15:19:23.808194",
55 "dependencies": [], 29 "dependencies": [],
56 "exit_code": 0, 30 "exit_code": 0,
57 "external_id": "151742", 31 "external_id": "300911",
58 "galaxy_version": "24.2", 32 "galaxy_version": "24.2",
59 "handler": null, 33 "handler": null,
60 "history_id": "f16125b2a7e364b6", 34 "history_id": "e660c01bdba47572",
61 "id": "711290ccc3448dbe", 35 "id": "86d58b95f07edb2d",
62 "inputs": { 36 "inputs": {
63 "domestication_csv": { 37 "domestication_csv": {
64 "id": "aaa883914c50d913", 38 "id": "6c832fb8ac42860f",
65 "src": "hda", 39 "src": "hda",
66 "uuid": "8d08fc90-ab45-4d65-8912-1edef99b50e5" 40 "uuid": "fbc30e96-b97e-4267-8ed5-5ceaa219759e"
67 },
68 "genbank_files": {
69 "id": "f16125b2a7e364b6",
70 "src": "hda",
71 "uuid": "1773336e-37c8-467a-932e-47c5d4bc7247"
72 }, 41 },
73 "genbank_files1": { 42 "genbank_files1": {
74 "id": "f16125b2a7e364b6", 43 "id": "e660c01bdba47572",
75 "src": "hda", 44 "src": "hda",
76 "uuid": "1773336e-37c8-467a-932e-47c5d4bc7247" 45 "uuid": "98eaff26-0334-4311-b121-579c564457fa"
77 }, 46 },
78 "genbank_files2": { 47 "genbank_files2": {
79 "id": "723c01d174904c31", 48 "id": "94d973d69c111d7f",
80 "src": "hda", 49 "src": "hda",
81 "uuid": "ee4defe5-2762-48fb-b10b-350bfbb4b71d" 50 "uuid": "69e06834-aff3-45c0-8c8a-1b0951b3c58a"
82 }, 51 },
83 "genbank_files3": { 52 "genbank_files3": {
84 "id": "6f9854c84e6fb32c", 53 "id": "6da151567610da58",
85 "src": "hda", 54 "src": "hda",
86 "uuid": "4041b0a0-86b9-4a81-9e95-77031b1fb96f" 55 "uuid": "a43d91b4-75bc-42ad-b3eb-3c2b8974849d"
87 }, 56 },
88 "genbank_files4": { 57 "genbank_files4": {
89 "id": "ac6038717ee9c106", 58 "id": "2cbbdad9a9ee38a7",
90 "src": "hda", 59 "src": "hda",
91 "uuid": "fa8e14e1-6c87-4a13-801f-ecb72b5e9517" 60 "uuid": "b8425ed5-d152-443a-ab5e-d5e5d8e18685"
92 }, 61 },
93 "genbank_files5": { 62 "genbank_files5": {
94 "id": "1b3b4b31ea959cca", 63 "id": "8cbbf46d79fe2594",
95 "src": "hda", 64 "src": "hda",
96 "uuid": "07b8841b-22ef-4142-8931-7ae4111f1887" 65 "uuid": "af5ff6ae-e7f3-4d04-9e27-2f4619b9a7f5"
97 }, 66 },
98 "genbank_files6": { 67 "genbank_files6": {
99 "id": "7144c3d02f40c0d6", 68 "id": "8e76e08000cb23f6",
100 "src": "hda", 69 "src": "hda",
101 "uuid": "a653f705-9192-485d-94f3-22b66714c9fb" 70 "uuid": "dfbae617-1607-410e-ae63-95e367876898"
102 }, 71 },
103 "genbank_files7": { 72 "genbank_files7": {
104 "id": "9d14f67ce73d06b8", 73 "id": "c5a9d28d6cf64e0c",
105 "src": "hda", 74 "src": "hda",
106 "uuid": "1ea79cfa-b478-4c9b-b906-9b08526c85f4" 75 "uuid": "99d37e87-dd8a-4439-a03a-004433442d3f"
107 } 76 }
108 }, 77 },
109 "job_messages": [], 78 "job_messages": [],
110 "job_metrics": [], 79 "job_metrics": [],
111 "job_runner_name": null, 80 "job_runner_name": null,
113 "job_stdout": "", 82 "job_stdout": "",
114 "model_class": "Job", 83 "model_class": "Job",
115 "output_collections": {}, 84 "output_collections": {},
116 "outputs": { 85 "outputs": {
117 "output_zip": { 86 "output_zip": {
118 "id": "711290ccc3448dbe", 87 "id": "86d58b95f07edb2d",
119 "src": "hda", 88 "src": "hda",
120 "uuid": "3bd2c885-c568-4c63-8f50-4d3f470c77a5" 89 "uuid": "6e663eda-900f-4c38-aa98-8ed6be291879"
121 } 90 }
122 }, 91 },
123 "params": { 92 "params": {
124 "__input_ext": "\"input\"", 93 "__input_ext": "\"input\"",
125 "adv": "{\"allow_edits\": true, \"use_file_names_as_ids\": true}", 94 "adv": "{\"allow_edits\": true, \"use_file_names_as_ids\": true}",
126 "chromInfo": "\"/tmp/tmpbjg5_060/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 95 "chromInfo": "\"/tmp/tmpmomj1390/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
127 "dbkey": "\"?\"", 96 "dbkey": "\"?\"",
97 "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}",
128 "methylation_protection": "false" 98 "methylation_protection": "false"
129 }, 99 },
130 "state": "ok", 100 "state": "ok",
131 "stderr": "\rrecord: 0%| | 0/7 [00:00<?, ?it/s, now=None]\rrecord: 43%|\u2588\u2588\u2588\u2588\u258e | 3/7 [00:01<00:02, 1.57it/s, now=None]\r \r", 101 "stderr": "\rrecord: 0%| | 0/7 [00:00<?, ?it/s, now=None]\rrecord: 43%|\u2588\u2588\u2588\u2588\u258e | 3/7 [00:01<00:02, 1.73it/s, now=None]\r \r",
132 "stdout": "Part names were not truncated\n", 102 "stdout": "Part names were not truncated\n",
133 "tool_id": "domestication", 103 "tool_id": "domestication",
134 "tool_stderr": "\rrecord: 0%| | 0/7 [00:00<?, ?it/s, now=None]\rrecord: 43%|\u2588\u2588\u2588\u2588\u258e | 3/7 [00:01<00:02, 1.57it/s, now=None]\r \r", 104 "tool_stderr": "\rrecord: 0%| | 0/7 [00:00<?, ?it/s, now=None]\rrecord: 43%|\u2588\u2588\u2588\u2588\u258e | 3/7 [00:01<00:02, 1.73it/s, now=None]\r \r",
135 "tool_stdout": "Part names were not truncated\n", 105 "tool_stdout": "Part names were not truncated\n",
136 "update_time": "2025-05-12T10:19:34.231647", 106 "update_time": "2025-05-12T15:19:35.066496",
137 "user_email": "planemo@galaxyproject.org", 107 "user_email": "planemo@galaxyproject.org",
138 "user_id": "f16125b2a7e364b6" 108 "user_id": "e660c01bdba47572"
139 }, 109 },
140 "status": "success", 110 "status": "success",
141 "test_index": 0, 111 "test_index": 0,
142 "time_seconds": 34.99027061462402, 112 "time_seconds": 33.88110899925232,
143 "tool_id": "domestication", 113 "tool_id": "domestication",
144 "tool_version": "0.1.0+galaxy0" 114 "tool_version": "0.1.0+galaxy1"
145 }, 115 },
146 "has_data": true, 116 "has_data": true,
147 "id": "domestication-0" 117 "id": "domestication-0"
148 }, 118 },
149 { 119 {
150 "data": { 120 "data": {
151 "inputs": { 121 "inputs": {
152 "adv|allow_edits": true, 122 "adv|allow_edits": true,
153 "adv|use_file_names_as_ids": true, 123 "adv|use_file_names_as_ids": true,
154 "domestication_csv": { 124 "domestication_csv": {
155 "id": "0712ecd128ea57d7", 125 "id": "ff21cf4b5818da45",
156 "src": "hda" 126 "src": "hda"
157 }, 127 },
158 "genbank_files": [ 128 "genbank_files": {
159 { 129 "id": "94d973d69c111d7f",
160 "id": "4e411fc6241b00c0", 130 "src": "hdca"
161 "src": "hda" 131 },
162 },
163 {
164 "id": "53c1d5da63e22734",
165 "src": "hda"
166 },
167 {
168 "id": "918757d2d9059ecb",
169 "src": "hda"
170 },
171 {
172 "id": "3d0b1ede0f9f407d",
173 "src": "hda"
174 },
175 {
176 "id": "d67f207c70f90bba",
177 "src": "hda"
178 },
179 {
180 "id": "5c88b35f288963f6",
181 "src": "hda"
182 },
183 {
184 "id": "3e3b5a8a813595d7",
185 "src": "hda"
186 }
187 ],
188 "methylation_protection": true 132 "methylation_protection": true
189 }, 133 },
190 "job": { 134 "job": {
191 "command_line": "mkdir 'outdir_gb' && mkdir 'outdir_zip' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpbjg5_060/files/b/f/f/dataset_bff36fb4-2ddc-497c-a812-b821fcafcaf6.dat,/tmp/tmpbjg5_060/files/c/9/4/dataset_c94619a2-c571-4719-8d77-fe8e5566092f.dat,/tmp/tmpbjg5_060/files/a/8/e/dataset_a8edcb78-9ec5-45f1-b05f-17b619e372a7.dat,/tmp/tmpbjg5_060/files/b/c/6/dataset_bc62ddd0-de10-42c4-9aa4-c62010af835d.dat,/tmp/tmpbjg5_060/files/5/5/a/dataset_55aa74b8-36ca-474d-ac73-bda39d9e5e01.dat,/tmp/tmpbjg5_060/files/7/0/9/dataset_7098d987-4200-4111-9508-bbe109fec271.dat,/tmp/tmpbjg5_060/files/7/8/1/dataset_781da4ba-2cb5-4cc3-aebb-e066475dfaef.dat' --csv_file '/tmp/tmpbjg5_060/files/6/2/b/dataset_62b232e6-6915-467a-9e55-febd6b17d9d7.dat' --file_name_mapping '/tmp/tmpbjg5_060/files/b/f/f/dataset_bff36fb4-2ddc-497c-a812-b821fcafcaf6.dat:p3_2_CAG.gb,/tmp/tmpbjg5_060/files/c/9/4/dataset_c94619a2-c571-4719-8d77-fe8e5566092f.dat:p7_gfp_sequence.gb,/tmp/tmpbjg5_060/files/a/8/e/dataset_a8edcb78-9ec5-45f1-b05f-17b619e372a7.dat:p14_CMVp.gb,/tmp/tmpbjg5_060/files/b/c/6/dataset_bc62ddd0-de10-42c4-9aa4-c62010af835d.dat:p16_bGHpolyA.gb,/tmp/tmpbjg5_060/files/5/5/a/dataset_55aa74b8-36ca-474d-ac73-bda39d9e5e01.dat:p18_CMVp.gb,/tmp/tmpbjg5_060/files/7/0/9/dataset_7098d987-4200-4111-9508-bbe109fec271.dat:p19_mNeoGreen.gb,/tmp/tmpbjg5_060/files/7/8/1/dataset_781da4ba-2cb5-4cc3-aebb-e066475dfaef.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_methprot 'outdir_gb' --methylation_protection 'true' && cp 'output_zip.zip' '/tmp/tmpbjg5_060/job_working_directory/000/18/outputs/dataset_8986a1c0-102c-469b-b20d-012bfab02e3a.dat'", 135 "command_line": "mkdir 'outdir_gb' && mkdir 'outdir_zip' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpmomj1390/files/b/1/3/dataset_b13b6d1b-090f-499c-b64b-c1630dcc675b.dat,/tmp/tmpmomj1390/files/c/5/0/dataset_c5065ec8-dc8a-4bd5-ad78-8b6925b1e13a.dat,/tmp/tmpmomj1390/files/5/c/6/dataset_5c6a4082-6f02-474d-be70-1263d3220dcb.dat,/tmp/tmpmomj1390/files/a/b/1/dataset_ab14cebb-85b9-4fff-9cb1-1056c9701e21.dat,/tmp/tmpmomj1390/files/6/f/e/dataset_6fe23d92-e2c0-4888-b627-d413e61b1d61.dat,/tmp/tmpmomj1390/files/e/9/9/dataset_e990dda1-9ebf-4414-a79c-9cf220f81ca3.dat,/tmp/tmpmomj1390/files/b/4/0/dataset_b40f7a77-27cd-4422-b821-eecc5774e6e6.dat' --csv_file '/tmp/tmpmomj1390/files/0/b/1/dataset_0b1c2aef-600f-4d98-afa3-a2243e337da1.dat' --file_name_mapping '/tmp/tmpmomj1390/files/b/1/3/dataset_b13b6d1b-090f-499c-b64b-c1630dcc675b.dat:p3_2_CAG.gb,/tmp/tmpmomj1390/files/c/5/0/dataset_c5065ec8-dc8a-4bd5-ad78-8b6925b1e13a.dat:p7_gfp_sequence.gb,/tmp/tmpmomj1390/files/5/c/6/dataset_5c6a4082-6f02-474d-be70-1263d3220dcb.dat:p14_CMVp.gb,/tmp/tmpmomj1390/files/a/b/1/dataset_ab14cebb-85b9-4fff-9cb1-1056c9701e21.dat:p16_bGHpolyA.gb,/tmp/tmpmomj1390/files/6/f/e/dataset_6fe23d92-e2c0-4888-b627-d413e61b1d61.dat:p18_CMVp.gb,/tmp/tmpmomj1390/files/e/9/9/dataset_e990dda1-9ebf-4414-a79c-9cf220f81ca3.dat:p19_mNeoGreen.gb,/tmp/tmpmomj1390/files/b/4/0/dataset_b40f7a77-27cd-4422-b821-eecc5774e6e6.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_methprot 'outdir_gb' --methylation_protection 'true' && cp 'output_zip.zip' '/tmp/tmpmomj1390/job_working_directory/000/18/outputs/dataset_e5fbb54d-ef6f-4bd9-9a45-a16d722f41f1.dat'",
192 "command_version": "", 136 "command_version": "",
193 "copied_from_job_id": null, 137 "copied_from_job_id": null,
194 "create_time": "2025-05-12T10:19:57.856904", 138 "create_time": "2025-05-12T15:19:57.567258",
195 "dependencies": [ 139 "dependencies": [
196 { 140 {
197 "cacheable": false, 141 "cacheable": false,
198 "dependency_resolver": { 142 "dependency_resolver": {
199 "auto_init": true, 143 "auto_init": true,
207 "resolves_simple_dependencies": true, 151 "resolves_simple_dependencies": true,
208 "use_local": false, 152 "use_local": false,
209 "versionless": false 153 "versionless": false
210 }, 154 },
211 "dependency_type": "conda", 155 "dependency_type": "conda",
212 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-bdd4a85f8bf182a44b33909cd353bfe9976ca4f7cd7e03cfde43ddec0191410c", 156 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-f05e814ead139eea2d366bbe58573083f8fc211e23465a99188722aaf9b8befd",
213 "exact": true, 157 "exact": true,
214 "model_class": "MergedCondaDependency", 158 "model_class": "MergedCondaDependency",
215 "name": "flametree", 159 "name": "flametree",
216 "version": "0.1.11" 160 "version": "0.1.11"
217 }, 161 },
229 "resolves_simple_dependencies": true, 173 "resolves_simple_dependencies": true,
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231 "versionless": false 175 "versionless": false
232 }, 176 },
233 "dependency_type": "conda", 177 "dependency_type": "conda",
234 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-bdd4a85f8bf182a44b33909cd353bfe9976ca4f7cd7e03cfde43ddec0191410c", 178 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-f05e814ead139eea2d366bbe58573083f8fc211e23465a99188722aaf9b8befd",
235 "exact": true, 179 "exact": true,
236 "model_class": "MergedCondaDependency", 180 "model_class": "MergedCondaDependency",
237 "name": "biopython", 181 "name": "biopython",
238 "version": "1.85" 182 "version": "1.85"
239 }, 183 },
251 "resolves_simple_dependencies": true, 195 "resolves_simple_dependencies": true,
252 "use_local": false, 196 "use_local": false,
253 "versionless": false 197 "versionless": false
254 }, 198 },
255 "dependency_type": "conda", 199 "dependency_type": "conda",
256 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-bdd4a85f8bf182a44b33909cd353bfe9976ca4f7cd7e03cfde43ddec0191410c", 200 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-f05e814ead139eea2d366bbe58573083f8fc211e23465a99188722aaf9b8befd",
257 "exact": true, 201 "exact": true,
258 "model_class": "MergedCondaDependency", 202 "model_class": "MergedCondaDependency",
259 "name": "proglog", 203 "name": "proglog",
260 "version": "0.1.10" 204 "version": "0.1.10"
261 }, 205 },
273 "resolves_simple_dependencies": true, 217 "resolves_simple_dependencies": true,
274 "use_local": false, 218 "use_local": false,
275 "versionless": false 219 "versionless": false
276 }, 220 },
277 "dependency_type": "conda", 221 "dependency_type": "conda",
278 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-bdd4a85f8bf182a44b33909cd353bfe9976ca4f7cd7e03cfde43ddec0191410c", 222 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-f05e814ead139eea2d366bbe58573083f8fc211e23465a99188722aaf9b8befd",
279 "exact": true, 223 "exact": true,
280 "model_class": "MergedCondaDependency", 224 "model_class": "MergedCondaDependency",
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282 "version": "0.2.1" 226 "version": "0.2.1"
283 }, 227 },
295 "resolves_simple_dependencies": true, 239 "resolves_simple_dependencies": true,
296 "use_local": false, 240 "use_local": false,
297 "versionless": false 241 "versionless": false
298 }, 242 },
299 "dependency_type": "conda", 243 "dependency_type": "conda",
300 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-bdd4a85f8bf182a44b33909cd353bfe9976ca4f7cd7e03cfde43ddec0191410c", 244 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-f05e814ead139eea2d366bbe58573083f8fc211e23465a99188722aaf9b8befd",
301 "exact": true, 245 "exact": true,
302 "model_class": "MergedCondaDependency", 246 "model_class": "MergedCondaDependency",
303 "name": "pandas", 247 "name": "pandas",
304 "version": "2.2.3" 248 "version": "2.2.3"
305 }, 249 },
317 "resolves_simple_dependencies": true, 261 "resolves_simple_dependencies": true,
318 "use_local": false, 262 "use_local": false,
319 "versionless": false 263 "versionless": false
320 }, 264 },
321 "dependency_type": "conda", 265 "dependency_type": "conda",
322 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-bdd4a85f8bf182a44b33909cd353bfe9976ca4f7cd7e03cfde43ddec0191410c", 266 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-f05e814ead139eea2d366bbe58573083f8fc211e23465a99188722aaf9b8befd",
323 "exact": true, 267 "exact": true,
324 "model_class": "MergedCondaDependency", 268 "model_class": "MergedCondaDependency",
325 "name": "dnacauldron", 269 "name": "dnacauldron",
326 "version": "2.0.11" 270 "version": "2.0.11"
327 }, 271 },
339 "resolves_simple_dependencies": true, 283 "resolves_simple_dependencies": true,
340 "use_local": false, 284 "use_local": false,
341 "versionless": false 285 "versionless": false
342 }, 286 },
343 "dependency_type": "conda", 287 "dependency_type": "conda",
344 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-bdd4a85f8bf182a44b33909cd353bfe9976ca4f7cd7e03cfde43ddec0191410c", 288 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-f05e814ead139eea2d366bbe58573083f8fc211e23465a99188722aaf9b8befd",
345 "exact": true, 289 "exact": true,
346 "model_class": "MergedCondaDependency", 290 "model_class": "MergedCondaDependency",
347 "name": "pdf-reports", 291 "name": "pdf-reports",
348 "version": "0.3.9" 292 "version": "0.3.9"
349 }, 293 },
361 "resolves_simple_dependencies": true, 305 "resolves_simple_dependencies": true,
362 "use_local": false, 306 "use_local": false,
363 "versionless": false 307 "versionless": false
364 }, 308 },
365 "dependency_type": "conda", 309 "dependency_type": "conda",
366 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-bdd4a85f8bf182a44b33909cd353bfe9976ca4f7cd7e03cfde43ddec0191410c", 310 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-f05e814ead139eea2d366bbe58573083f8fc211e23465a99188722aaf9b8befd",
367 "exact": true, 311 "exact": true,
368 "model_class": "MergedCondaDependency", 312 "model_class": "MergedCondaDependency",
369 "name": "sequenticon", 313 "name": "sequenticon",
370 "version": "0.1.7" 314 "version": "0.1.8"
371 }, 315 },
372 { 316 {
373 "cacheable": false, 317 "cacheable": false,
374 "dependency_resolver": { 318 "dependency_resolver": {
375 "auto_init": true, 319 "auto_init": true,
376 "auto_install": true, 320 "auto_install": true,
377 "can_uninstall_dependencies": true, 321 "can_uninstall_dependencies": true,
378 "ensure_channels": "conda-forge,bioconda", 322 "ensure_channels": "conda-forge,bioconda",
379 "model_class": "CondaDependencyResolver", 323 "model_class": "CondaDependencyResolver",
380 "prefix": "/home/rkhaled/miniconda3", 324 "prefix": "/home/rkhaled/miniconda3",
381 "read_only": false, 325 "read_only": false,
382 "resolver_type": "conda", 326 "resolver_type": "conda",
383 "resolves_simple_dependencies": true, 327 "resolves_simple_dependencies": true,
384 "use_local": false, 328 "use_local": false,
385 "versionless": false 329 "versionless": false
386 }, 330 },
387 "dependency_type": "conda", 331 "dependency_type": "conda",
388 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-bdd4a85f8bf182a44b33909cd353bfe9976ca4f7cd7e03cfde43ddec0191410c", 332 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-f05e814ead139eea2d366bbe58573083f8fc211e23465a99188722aaf9b8befd",
389 "exact": true, 333 "exact": true,
390 "model_class": "MergedCondaDependency", 334 "model_class": "MergedCondaDependency",
391 "name": "dna_features_viewer", 335 "name": "dna_features_viewer",
392 "version": "3.1.4" 336 "version": "3.1.4"
393 } 337 }
394 ], 338 ],
395 "exit_code": 0, 339 "exit_code": 0,
396 "external_id": "152624", 340 "external_id": "301662",
397 "galaxy_version": "24.2", 341 "galaxy_version": "24.2",
398 "handler": null, 342 "handler": null,
399 "history_id": "723c01d174904c31", 343 "history_id": "94d973d69c111d7f",
400 "id": "297141c205679f60", 344 "id": "3a6ea217cbbcfeb3",
401 "inputs": { 345 "inputs": {
402 "domestication_csv": { 346 "domestication_csv": {
403 "id": "0712ecd128ea57d7", 347 "id": "ff21cf4b5818da45",
404 "src": "hda", 348 "src": "hda",
405 "uuid": "62b232e6-6915-467a-9e55-febd6b17d9d7" 349 "uuid": "0b1c2aef-600f-4d98-afa3-a2243e337da1"
406 },
407 "genbank_files": {
408 "id": "4e411fc6241b00c0",
409 "src": "hda",
410 "uuid": "bff36fb4-2ddc-497c-a812-b821fcafcaf6"
411 }, 350 },
412 "genbank_files1": { 351 "genbank_files1": {
413 "id": "4e411fc6241b00c0", 352 "id": "58b9ec2cc51a7bbc",
414 "src": "hda", 353 "src": "hda",
415 "uuid": "bff36fb4-2ddc-497c-a812-b821fcafcaf6" 354 "uuid": "b13b6d1b-090f-499c-b64b-c1630dcc675b"
416 }, 355 },
417 "genbank_files2": { 356 "genbank_files2": {
418 "id": "53c1d5da63e22734", 357 "id": "dfd200964bc0e0b3",
419 "src": "hda", 358 "src": "hda",
420 "uuid": "c94619a2-c571-4719-8d77-fe8e5566092f" 359 "uuid": "c5065ec8-dc8a-4bd5-ad78-8b6925b1e13a"
421 }, 360 },
422 "genbank_files3": { 361 "genbank_files3": {
423 "id": "918757d2d9059ecb", 362 "id": "728ee4548f790253",
424 "src": "hda", 363 "src": "hda",
425 "uuid": "a8edcb78-9ec5-45f1-b05f-17b619e372a7" 364 "uuid": "5c6a4082-6f02-474d-be70-1263d3220dcb"
426 }, 365 },
427 "genbank_files4": { 366 "genbank_files4": {
428 "id": "3d0b1ede0f9f407d", 367 "id": "8ec4d60703928c0b",
429 "src": "hda", 368 "src": "hda",
430 "uuid": "bc62ddd0-de10-42c4-9aa4-c62010af835d" 369 "uuid": "ab14cebb-85b9-4fff-9cb1-1056c9701e21"
431 }, 370 },
432 "genbank_files5": { 371 "genbank_files5": {
433 "id": "d67f207c70f90bba", 372 "id": "0ea49e46b3b36fc8",
434 "src": "hda", 373 "src": "hda",
435 "uuid": "55aa74b8-36ca-474d-ac73-bda39d9e5e01" 374 "uuid": "6fe23d92-e2c0-4888-b627-d413e61b1d61"
436 }, 375 },
437 "genbank_files6": { 376 "genbank_files6": {
438 "id": "5c88b35f288963f6", 377 "id": "fa15c2af129b8b76",
439 "src": "hda", 378 "src": "hda",
440 "uuid": "7098d987-4200-4111-9508-bbe109fec271" 379 "uuid": "e990dda1-9ebf-4414-a79c-9cf220f81ca3"
441 }, 380 },
442 "genbank_files7": { 381 "genbank_files7": {
443 "id": "3e3b5a8a813595d7", 382 "id": "e23a32c230113bee",
444 "src": "hda", 383 "src": "hda",
445 "uuid": "781da4ba-2cb5-4cc3-aebb-e066475dfaef" 384 "uuid": "b40f7a77-27cd-4422-b821-eecc5774e6e6"
446 } 385 }
447 }, 386 },
448 "job_messages": [], 387 "job_messages": [],
449 "job_metrics": [], 388 "job_metrics": [],
450 "job_runner_name": null, 389 "job_runner_name": null,
451 "job_stderr": "", 390 "job_stderr": "",
452 "job_stdout": "", 391 "job_stdout": "",
453 "model_class": "Job", 392 "model_class": "Job",
454 "output_collections": { 393 "output_collections": {
455 "methprot_gb": { 394 "methprot_gb": {
456 "id": "f16125b2a7e364b6", 395 "id": "6da151567610da58",
457 "src": "hdca" 396 "src": "hdca"
458 } 397 }
459 }, 398 },
460 "outputs": { 399 "outputs": {
461 "__new_primary_file_methprot_gb|p14_CMVp__": { 400 "__new_primary_file_methprot_gb|p14_CMVp__": {
462 "id": "85982e889452a524", 401 "id": "ff56119d03b36f7e",
463 "src": "hda", 402 "src": "hda",
464 "uuid": "4a810eb2-bc3c-4905-8f07-90f63a0b221f" 403 "uuid": "4ce1c883-a9a0-4d2f-893d-1367d70461a9"
465 }, 404 },
466 "__new_primary_file_methprot_gb|p16_bGHpolyA__": { 405 "__new_primary_file_methprot_gb|p16_bGHpolyA__": {
467 "id": "df7e9e960b92dcd6", 406 "id": "23c852ea5c29414c",
468 "src": "hda", 407 "src": "hda",
469 "uuid": "7e5476ac-38cd-4a82-98ad-0fc2222e49df" 408 "uuid": "1db47dfa-c46a-47cd-bd6e-cb373414291a"
470 }, 409 },
471 "__new_primary_file_methprot_gb|p18_CMVp__": { 410 "__new_primary_file_methprot_gb|p18_CMVp__": {
472 "id": "ff4a37beb4d084ef", 411 "id": "2a13f3a02c150685",
473 "src": "hda", 412 "src": "hda",
474 "uuid": "c8b8371f-c832-4287-8493-a58191a6dafc" 413 "uuid": "974bb633-efcf-4a64-8b65-ccd2e02c7fc7"
475 }, 414 },
476 "__new_primary_file_methprot_gb|p19_mNeoGreen__": { 415 "__new_primary_file_methprot_gb|p19_mNeoGreen__": {
477 "id": "72bf0a10e7ee2b0b", 416 "id": "0d219ad454277643",
478 "src": "hda", 417 "src": "hda",
479 "uuid": "cb0cb9ab-3856-4998-80d8-c790704d0ea6" 418 "uuid": "bc97a0eb-f620-4e9c-8d54-f538c86a1a84"
480 }, 419 },
481 "__new_primary_file_methprot_gb|p22_PGKpolyA__": { 420 "__new_primary_file_methprot_gb|p22_PGKpolyA__": {
482 "id": "24c3dd01ebb16d97", 421 "id": "8ba22fe1db24a1dd",
483 "src": "hda", 422 "src": "hda",
484 "uuid": "08cbae4f-3b7c-4443-b181-b53764c22971" 423 "uuid": "f2082e29-29a9-44b5-8090-88d82b96fab7"
485 }, 424 },
486 "__new_primary_file_methprot_gb|p3_2_CAG__": { 425 "__new_primary_file_methprot_gb|p3_2_CAG__": {
487 "id": "93cd9bd35f8d4a08", 426 "id": "eeb9f7bb54b54cc1",
488 "src": "hda", 427 "src": "hda",
489 "uuid": "d2ff7a41-e0f9-4bea-bc4c-cc7ff6f22836" 428 "uuid": "996aeeed-114f-4e88-a3e8-ac6ca810bd5a"
490 }, 429 },
491 "__new_primary_file_methprot_gb|p7_gfp_sequence__": { 430 "__new_primary_file_methprot_gb|p7_gfp_sequence__": {
492 "id": "78c1a7160169fd44", 431 "id": "a067f4d569f90edf",
493 "src": "hda", 432 "src": "hda",
494 "uuid": "6c4d9b0d-486a-4c36-9670-e2266d5a9622" 433 "uuid": "938ac53e-c913-4c4e-99b5-0ed92e4114d4"
495 }, 434 },
496 "output_zip": { 435 "output_zip": {
497 "id": "297141c205679f60", 436 "id": "3a6ea217cbbcfeb3",
498 "src": "hda", 437 "src": "hda",
499 "uuid": "8986a1c0-102c-469b-b20d-012bfab02e3a" 438 "uuid": "e5fbb54d-ef6f-4bd9-9a45-a16d722f41f1"
500 } 439 }
501 }, 440 },
502 "params": { 441 "params": {
503 "__input_ext": "\"input\"", 442 "__input_ext": "\"input\"",
504 "adv": "{\"allow_edits\": true, \"use_file_names_as_ids\": true}", 443 "adv": "{\"allow_edits\": true, \"use_file_names_as_ids\": true}",
505 "chromInfo": "\"/tmp/tmpbjg5_060/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 444 "chromInfo": "\"/tmp/tmpmomj1390/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
506 "dbkey": "\"?\"", 445 "dbkey": "\"?\"",
446 "genbank_files": "{\"values\": [{\"id\": 2, \"src\": \"hdca\"}]}",
507 "methylation_protection": "true" 447 "methylation_protection": "true"
508 }, 448 },
509 "state": "ok", 449 "state": "ok",
510 "stderr": "\rrecord: 0%| | 0/7 [00:00<?, ?it/s, now=None]\rrecord: 43%|\u2588\u2588\u2588\u2588\u258e | 3/7 [00:01<00:02, 1.70it/s, now=None]\r \r", 450 "stderr": "\rrecord: 0%| | 0/7 [00:00<?, ?it/s, now=None]\rrecord: 43%|\u2588\u2588\u2588\u2588\u258e | 3/7 [00:01<00:02, 1.76it/s, now=None]\r \r",
511 "stdout": "Part names were not truncated\n", 451 "stdout": "Part names were not truncated\n",
512 "tool_id": "domestication", 452 "tool_id": "domestication",
513 "tool_stderr": "\rrecord: 0%| | 0/7 [00:00<?, ?it/s, now=None]\rrecord: 43%|\u2588\u2588\u2588\u2588\u258e | 3/7 [00:01<00:02, 1.70it/s, now=None]\r \r", 453 "tool_stderr": "\rrecord: 0%| | 0/7 [00:00<?, ?it/s, now=None]\rrecord: 43%|\u2588\u2588\u2588\u2588\u258e | 3/7 [00:01<00:02, 1.76it/s, now=None]\r \r",
514 "tool_stdout": "Part names were not truncated\n", 454 "tool_stdout": "Part names were not truncated\n",
515 "update_time": "2025-05-12T10:20:09.457096", 455 "update_time": "2025-05-12T15:20:08.233126",
516 "user_email": "planemo@galaxyproject.org", 456 "user_email": "planemo@galaxyproject.org",
517 "user_id": "f16125b2a7e364b6" 457 "user_id": "e660c01bdba47572"
518 }, 458 },
519 "status": "success", 459 "status": "success",
520 "test_index": 1, 460 "test_index": 1,
521 "time_seconds": 34.99931049346924, 461 "time_seconds": 33.191433906555176,
522 "tool_id": "domestication", 462 "tool_id": "domestication",
523 "tool_version": "0.1.0+galaxy0" 463 "tool_version": "0.1.0+galaxy1"
524 }, 464 },
525 "has_data": true, 465 "has_data": true,
526 "id": "domestication-1" 466 "id": "domestication-1"
527 } 467 }
528 ], 468 ],