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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, 27 May 2025 08:08:21 +0000
parents 4bfdec0be6b1
children
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9:450ed9dca5d5 10:c52967fb95da
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": "3f0c528bcd0d2af0", 15 "id": "df3910bf12e3ecf9",
16 "src": "hda" 16 "src": "hda"
17 }, 17 },
18 "genbank_files": { 18 "genbank_files": {
19 "id": "2d588720727ac897", 19 "id": "40971d80b8a8a53c",
20 "src": "hdca" 20 "src": "hdca"
21 }, 21 },
22 "methylation_protection": false 22 "methylation_protection": false
23 }, 23 },
24 "job": { 24 "job": {
25 "command_line": "mkdir 'metoutdir_gb' && mkdir 'outdir_zip' && mkdir 'outdir_gb'&& cp '/tmp/tmpa__rr6q2/files/1/8/d/dataset_18d1bdeb-a69c-4f9a-8d59-4d4d12fbff4c.dat' 'domestication_csv.csv' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpa__rr6q2/files/f/3/b/dataset_f3b3d5cf-5f7f-4a6d-8c94-e7927144f3eb.dat,/tmp/tmpa__rr6q2/files/f/f/6/dataset_ff62cd6f-ecf0-46ea-ac72-3cc78a217ef8.dat,/tmp/tmpa__rr6q2/files/8/c/d/dataset_8cd82e26-da60-4c91-bb80-d65d9ac0864d.dat,/tmp/tmpa__rr6q2/files/a/f/6/dataset_af6f5158-3c00-4e30-a07f-b9cee1381d6c.dat,/tmp/tmpa__rr6q2/files/b/9/7/dataset_b97d206b-3b81-41ad-96a6-462a3ebcbbf2.dat,/tmp/tmpa__rr6q2/files/a/8/9/dataset_a8913c13-0cca-4e1e-9496-2c7f0bbcc485.dat,/tmp/tmpa__rr6q2/files/6/c/c/dataset_6cc8ecc8-2001-4b71-8cd5-3d42f368a626.dat' --csv_file 'domestication_csv.csv' --file_name_mapping '/tmp/tmpa__rr6q2/files/f/3/b/dataset_f3b3d5cf-5f7f-4a6d-8c94-e7927144f3eb.dat:p3_2_CAG.gb,/tmp/tmpa__rr6q2/files/f/f/6/dataset_ff62cd6f-ecf0-46ea-ac72-3cc78a217ef8.dat:p7_gfp_sequence.gb,/tmp/tmpa__rr6q2/files/8/c/d/dataset_8cd82e26-da60-4c91-bb80-d65d9ac0864d.dat:p14_CMVp.gb,/tmp/tmpa__rr6q2/files/a/f/6/dataset_af6f5158-3c00-4e30-a07f-b9cee1381d6c.dat:p16_bGHpolyA.gb,/tmp/tmpa__rr6q2/files/b/9/7/dataset_b97d206b-3b81-41ad-96a6-462a3ebcbbf2.dat:p18_CMVp.gb,/tmp/tmpa__rr6q2/files/a/8/9/dataset_a8913c13-0cca-4e1e-9496-2c7f0bbcc485.dat:p19_mNeoGreen.gb,/tmp/tmpa__rr6q2/files/6/c/c/dataset_6cc8ecc8-2001-4b71-8cd5-3d42f368a626.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_gb_dom 'outdir_gb' --output_methprot 'metoutdir_gb' --methylation_protection 'false' && cp 'output_zip.zip' '/tmp/tmpa__rr6q2/job_working_directory/000/9/outputs/dataset_3847af4a-c6f8-4bc2-92e6-a5111f36e863.dat'", 25 "command_line": "mkdir 'metoutdir_gb' && mkdir 'outdir_zip' && mkdir 'outdir_gb'&& cp '/tmp/tmpmo0pk3jj/files/6/1/a/dataset_61aea63f-fa8f-4855-b597-d298379d415c.dat' 'domestication_csv.csv' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpmo0pk3jj/files/2/f/f/dataset_2ff46bb9-5b06-4cad-b98f-afa1443697b5.dat,/tmp/tmpmo0pk3jj/files/9/9/c/dataset_99c508b5-234a-4eba-b9d2-05204eaa2ec8.dat,/tmp/tmpmo0pk3jj/files/0/a/0/dataset_0a0b7db9-a3ac-4999-b1c9-498618831d59.dat,/tmp/tmpmo0pk3jj/files/a/2/9/dataset_a2994595-0a40-48ba-a369-db577710e99a.dat,/tmp/tmpmo0pk3jj/files/c/8/b/dataset_c8b3e40f-a0a8-414e-a56c-bd71775b2218.dat,/tmp/tmpmo0pk3jj/files/c/8/1/dataset_c813a93e-97c6-4f6a-bcd0-dcdbd93728e2.dat,/tmp/tmpmo0pk3jj/files/3/6/8/dataset_368b2cf8-f34e-427d-888e-b431a4b28c87.dat' --csv_file 'domestication_csv.csv' --file_name_mapping '/tmp/tmpmo0pk3jj/files/2/f/f/dataset_2ff46bb9-5b06-4cad-b98f-afa1443697b5.dat:p3_2_CAG.gb,/tmp/tmpmo0pk3jj/files/9/9/c/dataset_99c508b5-234a-4eba-b9d2-05204eaa2ec8.dat:p7_gfp_sequence.gb,/tmp/tmpmo0pk3jj/files/0/a/0/dataset_0a0b7db9-a3ac-4999-b1c9-498618831d59.dat:p14_CMVp.gb,/tmp/tmpmo0pk3jj/files/a/2/9/dataset_a2994595-0a40-48ba-a369-db577710e99a.dat:p16_bGHpolyA.gb,/tmp/tmpmo0pk3jj/files/c/8/b/dataset_c8b3e40f-a0a8-414e-a56c-bd71775b2218.dat:p18_CMVp.gb,/tmp/tmpmo0pk3jj/files/c/8/1/dataset_c813a93e-97c6-4f6a-bcd0-dcdbd93728e2.dat:p19_mNeoGreen.gb,/tmp/tmpmo0pk3jj/files/3/6/8/dataset_368b2cf8-f34e-427d-888e-b431a4b28c87.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_gb_dom 'outdir_gb' --output_methprot 'metoutdir_gb' --methylation_protection 'false' && cp 'output_zip.zip' '/tmp/tmpmo0pk3jj/job_working_directory/000/9/outputs/dataset_598cd11f-0878-422d-b265-3e7d109f52d4.dat'",
26 "command_version": "", 26 "command_version": "",
27 "copied_from_job_id": null, 27 "copied_from_job_id": null,
28 "create_time": "2025-05-23T09:02:47.568318", 28 "create_time": "2025-05-27T08:07:08.549227",
29 "dependencies": [], 29 "dependencies": [],
30 "exit_code": 0, 30 "exit_code": 0,
31 "external_id": "59522", 31 "external_id": "15664",
32 "galaxy_version": "24.2", 32 "galaxy_version": "24.2",
33 "handler": null, 33 "handler": null,
34 "history_id": "2d588720727ac897", 34 "history_id": "40971d80b8a8a53c",
35 "id": "05d1fab5f2f95c6e", 35 "id": "beecbc66855f4047",
36 "inputs": { 36 "inputs": {
37 "domestication_csv": { 37 "domestication_csv": {
38 "id": "3f0c528bcd0d2af0", 38 "id": "df3910bf12e3ecf9",
39 "src": "hda", 39 "src": "hda",
40 "uuid": "18d1bdeb-a69c-4f9a-8d59-4d4d12fbff4c" 40 "uuid": "61aea63f-fa8f-4855-b597-d298379d415c"
41 }, 41 },
42 "genbank_files1": { 42 "genbank_files1": {
43 "id": "2d588720727ac897", 43 "id": "40971d80b8a8a53c",
44 "src": "hda", 44 "src": "hda",
45 "uuid": "f3b3d5cf-5f7f-4a6d-8c94-e7927144f3eb" 45 "uuid": "2ff46bb9-5b06-4cad-b98f-afa1443697b5"
46 }, 46 },
47 "genbank_files2": { 47 "genbank_files2": {
48 "id": "62972d51292f48e6", 48 "id": "722a3e09b8314bb2",
49 "src": "hda", 49 "src": "hda",
50 "uuid": "ff62cd6f-ecf0-46ea-ac72-3cc78a217ef8" 50 "uuid": "99c508b5-234a-4eba-b9d2-05204eaa2ec8"
51 }, 51 },
52 "genbank_files3": { 52 "genbank_files3": {
53 "id": "e362c0fcc265e8f8", 53 "id": "1cc8aca787b2436a",
54 "src": "hda", 54 "src": "hda",
55 "uuid": "8cd82e26-da60-4c91-bb80-d65d9ac0864d" 55 "uuid": "0a0b7db9-a3ac-4999-b1c9-498618831d59"
56 }, 56 },
57 "genbank_files4": { 57 "genbank_files4": {
58 "id": "9106613ee8ff8561", 58 "id": "8026227525c5f951",
59 "src": "hda", 59 "src": "hda",
60 "uuid": "af6f5158-3c00-4e30-a07f-b9cee1381d6c" 60 "uuid": "a2994595-0a40-48ba-a369-db577710e99a"
61 }, 61 },
62 "genbank_files5": { 62 "genbank_files5": {
63 "id": "0973ce805f0b9fc9", 63 "id": "38afb044c6b21b09",
64 "src": "hda", 64 "src": "hda",
65 "uuid": "b97d206b-3b81-41ad-96a6-462a3ebcbbf2" 65 "uuid": "c8b3e40f-a0a8-414e-a56c-bd71775b2218"
66 }, 66 },
67 "genbank_files6": { 67 "genbank_files6": {
68 "id": "3f7b9edb7f21ca84", 68 "id": "58f07e41a8a4674f",
69 "src": "hda", 69 "src": "hda",
70 "uuid": "a8913c13-0cca-4e1e-9496-2c7f0bbcc485" 70 "uuid": "c813a93e-97c6-4f6a-bcd0-dcdbd93728e2"
71 }, 71 },
72 "genbank_files7": { 72 "genbank_files7": {
73 "id": "898926e359e5028c", 73 "id": "3e34fe414480d6bc",
74 "src": "hda", 74 "src": "hda",
75 "uuid": "6cc8ecc8-2001-4b71-8cd5-3d42f368a626" 75 "uuid": "368b2cf8-f34e-427d-888e-b431a4b28c87"
76 } 76 }
77 }, 77 },
78 "job_messages": [], 78 "job_messages": [],
79 "job_metrics": [], 79 "job_metrics": [],
80 "job_runner_name": null, 80 "job_runner_name": null,
81 "job_stderr": "", 81 "job_stderr": "",
82 "job_stdout": "", 82 "job_stdout": "",
83 "model_class": "Job", 83 "model_class": "Job",
84 "output_collections": { 84 "output_collections": {
85 "domesticated_gb": { 85 "domesticated_gb": {
86 "id": "62972d51292f48e6", 86 "id": "722a3e09b8314bb2",
87 "src": "hdca" 87 "src": "hdca"
88 } 88 }
89 }, 89 },
90 "outputs": { 90 "outputs": {
91 "__new_primary_file_domesticated_gb|p14_CMVp__": { 91 "__new_primary_file_domesticated_gb|p14_CMVp__": {
92 "id": "0481fa54d30635c9", 92 "id": "8b52218386489a1b",
93 "src": "hda", 93 "src": "hda",
94 "uuid": "a0555d82-443f-4b4b-8431-2a9d4e049017" 94 "uuid": "9ec489c3-d7d2-4c8e-85ed-7c608bfffc49"
95 }, 95 },
96 "__new_primary_file_domesticated_gb|p16_bGHpolyA__": { 96 "__new_primary_file_domesticated_gb|p16_bGHpolyA__": {
97 "id": "813bd8a24377d169", 97 "id": "7df4279c30fbf11a",
98 "src": "hda", 98 "src": "hda",
99 "uuid": "e506a4e3-7524-4360-abe1-b49ed99833d7" 99 "uuid": "e56aa342-fc45-4a28-befa-290f5722a67c"
100 }, 100 },
101 "__new_primary_file_domesticated_gb|p18_CMVp__": { 101 "__new_primary_file_domesticated_gb|p18_CMVp__": {
102 "id": "d79d6af225946b08", 102 "id": "5a11a7ea1c4a0b78",
103 "src": "hda", 103 "src": "hda",
104 "uuid": "851cdd02-8f5a-400a-9b51-483c43d67028" 104 "uuid": "8beec3f0-36c6-4994-b890-35fbba7d1c32"
105 }, 105 },
106 "__new_primary_file_domesticated_gb|p19_mNeoGreen__": { 106 "__new_primary_file_domesticated_gb|p19_mNeoGreen__": {
107 "id": "3ab85ee8e71bbdd5", 107 "id": "f727b077209f6bea",
108 "src": "hda", 108 "src": "hda",
109 "uuid": "118d7f40-4850-466b-9f40-e360f1748011" 109 "uuid": "7309490c-224e-46b1-82d1-94102829a851"
110 }, 110 },
111 "__new_primary_file_domesticated_gb|p22_PGKpolyA__": { 111 "__new_primary_file_domesticated_gb|p22_PGKpolyA__": {
112 "id": "5480ebfe4604885a", 112 "id": "77c3effc68e335c0",
113 "src": "hda", 113 "src": "hda",
114 "uuid": "b82fcc71-a34f-44f8-9dcf-546a10a5f2d6" 114 "uuid": "4d4c783f-d229-44b3-af52-0e6616cd140b"
115 }, 115 },
116 "__new_primary_file_domesticated_gb|p3_2_CAG__": { 116 "__new_primary_file_domesticated_gb|p3_2_CAG__": {
117 "id": "f174fd93dd20b3fc", 117 "id": "a5683b91f8081320",
118 "src": "hda", 118 "src": "hda",
119 "uuid": "fa38ea29-3950-4e40-aed2-427b47597fc7" 119 "uuid": "08b3572e-4f1c-4fe3-ac3c-8dcf2ec05ce2"
120 }, 120 },
121 "__new_primary_file_domesticated_gb|p7_gfp_sequence__": { 121 "__new_primary_file_domesticated_gb|p7_gfp_sequence__": {
122 "id": "58f99e5516a773cd", 122 "id": "3e3b60188e62bb8d",
123 "src": "hda", 123 "src": "hda",
124 "uuid": "538b66c4-b4d0-41b8-9355-afadc944621c" 124 "uuid": "6fe9d54a-584a-470a-82a5-b16b0ed0b7e1"
125 }, 125 },
126 "output_zip": { 126 "domesticated_zip": {
127 "id": "05d1fab5f2f95c6e", 127 "id": "beecbc66855f4047",
128 "src": "hda", 128 "src": "hda",
129 "uuid": "3847af4a-c6f8-4bc2-92e6-a5111f36e863" 129 "uuid": "598cd11f-0878-422d-b265-3e7d109f52d4"
130 } 130 }
131 }, 131 },
132 "params": { 132 "params": {
133 "__input_ext": "\"input\"", 133 "__input_ext": "\"input\"",
134 "adv": "{\"allow_edits\": true, \"use_file_names_as_ids\": true}", 134 "adv": "{\"allow_edits\": true, \"use_file_names_as_ids\": true}",
135 "chromInfo": "\"/tmp/tmpa__rr6q2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 135 "chromInfo": "\"/tmp/tmpmo0pk3jj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
136 "dbkey": "\"?\"", 136 "dbkey": "\"?\"",
137 "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}", 137 "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}",
138 "methylation_protection": "false" 138 "methylation_protection": "false"
139 }, 139 },
140 "state": "ok", 140 "state": "ok",
141 "stderr": "\rrecord: 0%| | 0/7 [00:00<?, ?it/s, now=None]\rrecord: 43%|\u2588\u2588\u2588\u2588\u258e | 3/7 [00:01<00:02, 1.75it/s, now=None]\r \r", 141 "stderr": "\rrecord: 0%| | 0/7 [00:00<?, ?it/s, now=None]\rrecord: 43%|\u2588\u2588\u2588\u2588\u258e | 3/7 [00:01<00:02, 1.68it/s, now=None]\r \r",
142 "stdout": "Part names were not truncated\n", 142 "stdout": "Part names were not truncated\n",
143 "tool_id": "domestication", 143 "tool_id": "domestication",
144 "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, 1.75it/s, now=None]\r \r", 144 "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, 1.68it/s, now=None]\r \r",
145 "tool_stdout": "Part names were not truncated\n", 145 "tool_stdout": "Part names were not truncated\n",
146 "update_time": "2025-05-23T09:02:58.973787", 146 "update_time": "2025-05-27T08:07:20.210958",
147 "user_email": "planemo@galaxyproject.org", 147 "user_email": "planemo@galaxyproject.org",
148 "user_id": "2d588720727ac897" 148 "user_id": "40971d80b8a8a53c"
149 }, 149 },
150 "status": "success", 150 "status": "success",
151 "test_index": 0, 151 "test_index": 0,
152 "time_seconds": 34.70007658004761, 152 "time_seconds": 34.19329214096069,
153 "tool_id": "domestication", 153 "tool_id": "domestication",
154 "tool_version": "0.1.0+galaxy1" 154 "tool_version": "0.1.0+galaxy1"
155 }, 155 },
156 "has_data": true, 156 "has_data": true,
157 "id": "domestication-0" 157 "id": "domestication-0"
160 "data": { 160 "data": {
161 "inputs": { 161 "inputs": {
162 "adv|allow_edits": true, 162 "adv|allow_edits": true,
163 "adv|use_file_names_as_ids": true, 163 "adv|use_file_names_as_ids": true,
164 "domestication_csv": { 164 "domestication_csv": {
165 "id": "0ac23d4d0b88827c", 165 "id": "2d30278c16dd9bf8",
166 "src": "hda" 166 "src": "hda"
167 }, 167 },
168 "genbank_files": { 168 "genbank_files": {
169 "id": "e362c0fcc265e8f8", 169 "id": "1cc8aca787b2436a",
170 "src": "hdca" 170 "src": "hdca"
171 }, 171 },
172 "methylation_protection": true 172 "methylation_protection": true
173 }, 173 },
174 "job": { 174 "job": {
175 "command_line": "mkdir 'metoutdir_gb' && mkdir 'outdir_zip' && mkdir 'outdir_gb'&& cp '/tmp/tmpa__rr6q2/files/8/9/c/dataset_89c41e63-3985-4c33-9154-735d98f3f2bb.dat' 'domestication_csv.csv' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpa__rr6q2/files/3/7/a/dataset_37a61c0f-4043-404f-97c9-1b2e4b277a0b.dat,/tmp/tmpa__rr6q2/files/a/c/d/dataset_acd5b8cd-260a-4eed-bbaa-083097afd437.dat,/tmp/tmpa__rr6q2/files/b/4/2/dataset_b429cf4a-5fc0-4b2f-a27f-7b7d2da197dd.dat,/tmp/tmpa__rr6q2/files/6/4/3/dataset_643037ae-a752-4ce5-80e9-921fa8b24d3b.dat,/tmp/tmpa__rr6q2/files/d/c/e/dataset_dce00e9a-8b99-4bce-a1c2-b17377db99cf.dat,/tmp/tmpa__rr6q2/files/0/2/0/dataset_020c2948-6eb0-4860-b17b-a3f35d138965.dat,/tmp/tmpa__rr6q2/files/2/c/6/dataset_2c6f9cf6-bf93-4c97-9ea8-17ad34702969.dat' --csv_file 'domestication_csv.csv' --file_name_mapping '/tmp/tmpa__rr6q2/files/3/7/a/dataset_37a61c0f-4043-404f-97c9-1b2e4b277a0b.dat:p3_2_CAG.gb,/tmp/tmpa__rr6q2/files/a/c/d/dataset_acd5b8cd-260a-4eed-bbaa-083097afd437.dat:p7_gfp_sequence.gb,/tmp/tmpa__rr6q2/files/b/4/2/dataset_b429cf4a-5fc0-4b2f-a27f-7b7d2da197dd.dat:p14_CMVp.gb,/tmp/tmpa__rr6q2/files/6/4/3/dataset_643037ae-a752-4ce5-80e9-921fa8b24d3b.dat:p16_bGHpolyA.gb,/tmp/tmpa__rr6q2/files/d/c/e/dataset_dce00e9a-8b99-4bce-a1c2-b17377db99cf.dat:p18_CMVp.gb,/tmp/tmpa__rr6q2/files/0/2/0/dataset_020c2948-6eb0-4860-b17b-a3f35d138965.dat:p19_mNeoGreen.gb,/tmp/tmpa__rr6q2/files/2/c/6/dataset_2c6f9cf6-bf93-4c97-9ea8-17ad34702969.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_gb_dom 'outdir_gb' --output_methprot 'metoutdir_gb' --methylation_protection 'true' && cp 'output_zip.zip' '/tmp/tmpa__rr6q2/job_working_directory/000/18/outputs/dataset_257e63c3-87b5-459a-b118-921e6217abe8.dat'", 175 "command_line": "mkdir 'metoutdir_gb' && mkdir 'outdir_zip' && mkdir 'outdir_gb'&& cp '/tmp/tmpmo0pk3jj/files/8/8/c/dataset_88ce7dbb-b512-47e2-b4c4-a33e25f510f5.dat' 'domestication_csv.csv' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpmo0pk3jj/files/3/e/0/dataset_3e0edcaf-c663-4aaa-833b-4d28d353ff86.dat,/tmp/tmpmo0pk3jj/files/c/b/e/dataset_cbeb8071-98da-4bcd-829a-3eebaaec359e.dat,/tmp/tmpmo0pk3jj/files/1/9/9/dataset_199870d8-d8a6-4437-8843-802fe43f55a3.dat,/tmp/tmpmo0pk3jj/files/5/8/2/dataset_582e346f-d990-4e67-aa16-75c5854a9c4e.dat,/tmp/tmpmo0pk3jj/files/5/a/9/dataset_5a962295-b81c-4eac-95f9-cb9b715227ec.dat,/tmp/tmpmo0pk3jj/files/a/d/6/dataset_ad62bd0c-a6a8-40dc-b75e-5caff07b002f.dat,/tmp/tmpmo0pk3jj/files/2/4/6/dataset_2462927e-bb24-4865-b0d7-233193737d9b.dat' --csv_file 'domestication_csv.csv' --file_name_mapping '/tmp/tmpmo0pk3jj/files/3/e/0/dataset_3e0edcaf-c663-4aaa-833b-4d28d353ff86.dat:p3_2_CAG.gb,/tmp/tmpmo0pk3jj/files/c/b/e/dataset_cbeb8071-98da-4bcd-829a-3eebaaec359e.dat:p7_gfp_sequence.gb,/tmp/tmpmo0pk3jj/files/1/9/9/dataset_199870d8-d8a6-4437-8843-802fe43f55a3.dat:p14_CMVp.gb,/tmp/tmpmo0pk3jj/files/5/8/2/dataset_582e346f-d990-4e67-aa16-75c5854a9c4e.dat:p16_bGHpolyA.gb,/tmp/tmpmo0pk3jj/files/5/a/9/dataset_5a962295-b81c-4eac-95f9-cb9b715227ec.dat:p18_CMVp.gb,/tmp/tmpmo0pk3jj/files/a/d/6/dataset_ad62bd0c-a6a8-40dc-b75e-5caff07b002f.dat:p19_mNeoGreen.gb,/tmp/tmpmo0pk3jj/files/2/4/6/dataset_2462927e-bb24-4865-b0d7-233193737d9b.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_gb_dom 'outdir_gb' --output_methprot 'metoutdir_gb' --methylation_protection 'true' && cp 'output_zip.zip' '/tmp/tmpmo0pk3jj/job_working_directory/000/18/outputs/dataset_b8f77694-af17-44c7-8ca7-94039b4f9f10.dat'",
176 "command_version": "", 176 "command_version": "",
177 "copied_from_job_id": null, 177 "copied_from_job_id": null,
178 "create_time": "2025-05-23T09:03:22.156202", 178 "create_time": "2025-05-27T08:07:43.266253",
179 "dependencies": [ 179 "dependencies": [
180 { 180 {
181 "cacheable": false, 181 "cacheable": false,
182 "dependency_resolver": { 182 "dependency_resolver": {
183 "auto_init": true, 183 "auto_init": true,
375 "name": "dna_features_viewer", 375 "name": "dna_features_viewer",
376 "version": "3.1.5" 376 "version": "3.1.5"
377 } 377 }
378 ], 378 ],
379 "exit_code": 0, 379 "exit_code": 0,
380 "external_id": "60268", 380 "external_id": "16351",
381 "galaxy_version": "24.2", 381 "galaxy_version": "24.2",
382 "handler": null, 382 "handler": null,
383 "history_id": "62972d51292f48e6", 383 "history_id": "722a3e09b8314bb2",
384 "id": "e08d37863731003c", 384 "id": "6c90a7736cfec646",
385 "inputs": { 385 "inputs": {
386 "domestication_csv": { 386 "domestication_csv": {
387 "id": "0ac23d4d0b88827c", 387 "id": "2d30278c16dd9bf8",
388 "src": "hda", 388 "src": "hda",
389 "uuid": "89c41e63-3985-4c33-9154-735d98f3f2bb" 389 "uuid": "88ce7dbb-b512-47e2-b4c4-a33e25f510f5"
390 }, 390 },
391 "genbank_files1": { 391 "genbank_files1": {
392 "id": "55d915b26d3a354e", 392 "id": "92861e8424eabf5a",
393 "src": "hda", 393 "src": "hda",
394 "uuid": "37a61c0f-4043-404f-97c9-1b2e4b277a0b" 394 "uuid": "3e0edcaf-c663-4aaa-833b-4d28d353ff86"
395 }, 395 },
396 "genbank_files2": { 396 "genbank_files2": {
397 "id": "e08d37863731003c", 397 "id": "6c90a7736cfec646",
398 "src": "hda", 398 "src": "hda",
399 "uuid": "acd5b8cd-260a-4eed-bbaa-083097afd437" 399 "uuid": "cbeb8071-98da-4bcd-829a-3eebaaec359e"
400 }, 400 },
401 "genbank_files3": { 401 "genbank_files3": {
402 "id": "72fd2001a1c00c74", 402 "id": "d833721564461fe0",
403 "src": "hda", 403 "src": "hda",
404 "uuid": "b429cf4a-5fc0-4b2f-a27f-7b7d2da197dd" 404 "uuid": "199870d8-d8a6-4437-8843-802fe43f55a3"
405 }, 405 },
406 "genbank_files4": { 406 "genbank_files4": {
407 "id": "535975adfebcbd66", 407 "id": "bc67cca121169b32",
408 "src": "hda", 408 "src": "hda",
409 "uuid": "643037ae-a752-4ce5-80e9-921fa8b24d3b" 409 "uuid": "582e346f-d990-4e67-aa16-75c5854a9c4e"
410 }, 410 },
411 "genbank_files5": { 411 "genbank_files5": {
412 "id": "44c226435b38bb38", 412 "id": "2c119c7d607245b7",
413 "src": "hda", 413 "src": "hda",
414 "uuid": "dce00e9a-8b99-4bce-a1c2-b17377db99cf" 414 "uuid": "5a962295-b81c-4eac-95f9-cb9b715227ec"
415 }, 415 },
416 "genbank_files6": { 416 "genbank_files6": {
417 "id": "bbe178e57c4f8c81", 417 "id": "654b689f382d7faf",
418 "src": "hda", 418 "src": "hda",
419 "uuid": "020c2948-6eb0-4860-b17b-a3f35d138965" 419 "uuid": "ad62bd0c-a6a8-40dc-b75e-5caff07b002f"
420 }, 420 },
421 "genbank_files7": { 421 "genbank_files7": {
422 "id": "11bdfc4549627602", 422 "id": "848a7ec9db54f91c",
423 "src": "hda", 423 "src": "hda",
424 "uuid": "2c6f9cf6-bf93-4c97-9ea8-17ad34702969" 424 "uuid": "2462927e-bb24-4865-b0d7-233193737d9b"
425 } 425 }
426 }, 426 },
427 "job_messages": [], 427 "job_messages": [],
428 "job_metrics": [], 428 "job_metrics": [],
429 "job_runner_name": null, 429 "job_runner_name": null,
430 "job_stderr": "", 430 "job_stderr": "",
431 "job_stdout": "", 431 "job_stdout": "",
432 "model_class": "Job", 432 "model_class": "Job",
433 "output_collections": { 433 "output_collections": {
434 "methprot_gb": { 434 "methprot_gb": {
435 "id": "9106613ee8ff8561", 435 "id": "8026227525c5f951",
436 "src": "hdca" 436 "src": "hdca"
437 } 437 }
438 }, 438 },
439 "outputs": { 439 "outputs": {
440 "__new_primary_file_methprot_gb|p14_CMVp__": { 440 "__new_primary_file_methprot_gb|p14_CMVp__": {
441 "id": "63657e65b797e156", 441 "id": "552487cd77e5739b",
442 "src": "hda", 442 "src": "hda",
443 "uuid": "ff3d4f80-e86b-4391-b395-1f11f74883e0" 443 "uuid": "47a78a3c-f714-4a3b-baf6-db74ec3e57ec"
444 }, 444 },
445 "__new_primary_file_methprot_gb|p16_bGHpolyA__": { 445 "__new_primary_file_methprot_gb|p16_bGHpolyA__": {
446 "id": "7000d26bf45ffb00", 446 "id": "c150df1632d3bf7a",
447 "src": "hda", 447 "src": "hda",
448 "uuid": "0ea8ad54-9cee-4a88-9352-cbf201923fb8" 448 "uuid": "9ec7ff7e-c752-40ab-8e30-d00bce534323"
449 }, 449 },
450 "__new_primary_file_methprot_gb|p18_CMVp__": { 450 "__new_primary_file_methprot_gb|p18_CMVp__": {
451 "id": "36313fb553e6e307", 451 "id": "3b8df2fa2b4da081",
452 "src": "hda", 452 "src": "hda",
453 "uuid": "e6a1e8a2-1881-4ea9-9e2f-c2bc40a273a6" 453 "uuid": "ef3876f0-595c-4e36-b1d2-424ac4f3c495"
454 }, 454 },
455 "__new_primary_file_methprot_gb|p19_mNeoGreen__": { 455 "__new_primary_file_methprot_gb|p19_mNeoGreen__": {
456 "id": "12401c2b6811fee0", 456 "id": "ea8abe36fc9e84c6",
457 "src": "hda", 457 "src": "hda",
458 "uuid": "a73b7443-df14-4dea-84f3-381db57cca18" 458 "uuid": "d9db4707-d9a0-4578-861a-4536b24e3d55"
459 }, 459 },
460 "__new_primary_file_methprot_gb|p22_PGKpolyA__": { 460 "__new_primary_file_methprot_gb|p22_PGKpolyA__": {
461 "id": "0eb41dc2e09a8361", 461 "id": "195917444a0d1fd3",
462 "src": "hda", 462 "src": "hda",
463 "uuid": "67791634-ccbb-4984-82b6-5f6dabf17fd3" 463 "uuid": "ebcddc78-8aec-4aa7-a99f-1f6c98312abf"
464 }, 464 },
465 "__new_primary_file_methprot_gb|p3_2_CAG__": { 465 "__new_primary_file_methprot_gb|p3_2_CAG__": {
466 "id": "963b9ee6a9b85043", 466 "id": "07090fd15ab7700f",
467 "src": "hda", 467 "src": "hda",
468 "uuid": "a79b48fa-4414-4de6-9747-be228b0650ff" 468 "uuid": "f565adba-00b9-4476-a1dc-f917d7695ed7"
469 }, 469 },
470 "__new_primary_file_methprot_gb|p7_gfp_sequence__": { 470 "__new_primary_file_methprot_gb|p7_gfp_sequence__": {
471 "id": "3716318b258c039e", 471 "id": "181ca79c6e3f2d04",
472 "src": "hda", 472 "src": "hda",
473 "uuid": "3834e7e4-4365-4020-88d7-554281f0836f" 473 "uuid": "d36b2983-c229-453a-b3c5-d6e44ab877f5"
474 }, 474 },
475 "output_zip": { 475 "domesticated_zip": {
476 "id": "c2e357d169213b81", 476 "id": "bbfdb6491da014b1",
477 "src": "hda", 477 "src": "hda",
478 "uuid": "257e63c3-87b5-459a-b118-921e6217abe8" 478 "uuid": "b8f77694-af17-44c7-8ca7-94039b4f9f10"
479 } 479 }
480 }, 480 },
481 "params": { 481 "params": {
482 "__input_ext": "\"input\"", 482 "__input_ext": "\"input\"",
483 "adv": "{\"allow_edits\": true, \"use_file_names_as_ids\": true}", 483 "adv": "{\"allow_edits\": true, \"use_file_names_as_ids\": true}",
484 "chromInfo": "\"/tmp/tmpa__rr6q2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 484 "chromInfo": "\"/tmp/tmpmo0pk3jj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
485 "dbkey": "\"?\"", 485 "dbkey": "\"?\"",
486 "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}", 486 "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}",
487 "methylation_protection": "true" 487 "methylation_protection": "true"
488 }, 488 },
489 "state": "ok", 489 "state": "ok",
490 "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", 490 "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",
491 "stdout": "Part names were not truncated\n", 491 "stdout": "Part names were not truncated\n",
492 "tool_id": "domestication", 492 "tool_id": "domestication",
493 "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", 493 "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",
494 "tool_stdout": "Part names were not truncated\n", 494 "tool_stdout": "Part names were not truncated\n",
495 "update_time": "2025-05-23T09:03:33.301866", 495 "update_time": "2025-05-27T08:07:54.372698",
496 "user_email": "planemo@galaxyproject.org", 496 "user_email": "planemo@galaxyproject.org",
497 "user_id": "2d588720727ac897" 497 "user_id": "40971d80b8a8a53c"
498 }, 498 },
499 "status": "success", 499 "status": "success",
500 "test_index": 1, 500 "test_index": 1,
501 "time_seconds": 34.21326494216919, 501 "time_seconds": 34.02547550201416,
502 "tool_id": "domestication", 502 "tool_id": "domestication",
503 "tool_version": "0.1.0+galaxy1" 503 "tool_version": "0.1.0+galaxy1"
504 }, 504 },
505 "has_data": true, 505 "has_data": true,
506 "id": "domestication-1" 506 "id": "domestication-1"