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comparison output.json @ 0:8fd9af4cb080 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 Mon, 12 May 2025 10:21:24 +0000
parents
children bf8cd9487e33
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-1:000000000000 0:8fd9af4cb080
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 "adv|allow_edits": true,
13 "adv|use_file_names_as_ids": true,
14 "domestication_csv": {
15 "id": "aaa883914c50d913",
16 "src": "hda"
17 },
18 "genbank_files": [
19 {
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21 "src": "hda"
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23 {
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27 {
28 "id": "6f9854c84e6fb32c",
29 "src": "hda"
30 },
31 {
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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
49 },
50 "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'",
52 "command_version": "",
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54 "create_time": "2025-05-12T10:19:22.845477",
55 "dependencies": [],
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57 "external_id": "151742",
58 "galaxy_version": "24.2",
59 "handler": null,
60 "history_id": "f16125b2a7e364b6",
61 "id": "711290ccc3448dbe",
62 "inputs": {
63 "domestication_csv": {
64 "id": "aaa883914c50d913",
65 "src": "hda",
66 "uuid": "8d08fc90-ab45-4d65-8912-1edef99b50e5"
67 },
68 "genbank_files": {
69 "id": "f16125b2a7e364b6",
70 "src": "hda",
71 "uuid": "1773336e-37c8-467a-932e-47c5d4bc7247"
72 },
73 "genbank_files1": {
74 "id": "f16125b2a7e364b6",
75 "src": "hda",
76 "uuid": "1773336e-37c8-467a-932e-47c5d4bc7247"
77 },
78 "genbank_files2": {
79 "id": "723c01d174904c31",
80 "src": "hda",
81 "uuid": "ee4defe5-2762-48fb-b10b-350bfbb4b71d"
82 },
83 "genbank_files3": {
84 "id": "6f9854c84e6fb32c",
85 "src": "hda",
86 "uuid": "4041b0a0-86b9-4a81-9e95-77031b1fb96f"
87 },
88 "genbank_files4": {
89 "id": "ac6038717ee9c106",
90 "src": "hda",
91 "uuid": "fa8e14e1-6c87-4a13-801f-ecb72b5e9517"
92 },
93 "genbank_files5": {
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95 "src": "hda",
96 "uuid": "07b8841b-22ef-4142-8931-7ae4111f1887"
97 },
98 "genbank_files6": {
99 "id": "7144c3d02f40c0d6",
100 "src": "hda",
101 "uuid": "a653f705-9192-485d-94f3-22b66714c9fb"
102 },
103 "genbank_files7": {
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105 "src": "hda",
106 "uuid": "1ea79cfa-b478-4c9b-b906-9b08526c85f4"
107 }
108 },
109 "job_messages": [],
110 "job_metrics": [],
111 "job_runner_name": null,
112 "job_stderr": "",
113 "job_stdout": "",
114 "model_class": "Job",
115 "output_collections": {},
116 "outputs": {
117 "output_zip": {
118 "id": "711290ccc3448dbe",
119 "src": "hda",
120 "uuid": "3bd2c885-c568-4c63-8f50-4d3f470c77a5"
121 }
122 },
123 "params": {
124 "__input_ext": "\"input\"",
125 "adv": "{\"allow_edits\": true, \"use_file_names_as_ids\": true}",
126 "chromInfo": "\"/tmp/tmpbjg5_060/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
127 "dbkey": "\"?\"",
128 "methylation_protection": "false"
129 },
130 "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",
132 "stdout": "Part names were not truncated\n",
133 "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",
135 "tool_stdout": "Part names were not truncated\n",
136 "update_time": "2025-05-12T10:19:34.231647",
137 "user_email": "planemo@galaxyproject.org",
138 "user_id": "f16125b2a7e364b6"
139 },
140 "status": "success",
141 "test_index": 0,
142 "time_seconds": 34.99027061462402,
143 "tool_id": "domestication",
144 "tool_version": "0.1.0+galaxy0"
145 },
146 "has_data": true,
147 "id": "domestication-0"
148 },
149 {
150 "data": {
151 "inputs": {
152 "adv|allow_edits": true,
153 "adv|use_file_names_as_ids": true,
154 "domestication_csv": {
155 "id": "0712ecd128ea57d7",
156 "src": "hda"
157 },
158 "genbank_files": [
159 {
160 "id": "4e411fc6241b00c0",
161 "src": "hda"
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
189 },
190 "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'",
192 "command_version": "",
193 "copied_from_job_id": null,
194 "create_time": "2025-05-12T10:19:57.856904",
195 "dependencies": [
196 {
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198 "dependency_resolver": {
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200 "auto_install": true,
201 "can_uninstall_dependencies": true,
202 "ensure_channels": "conda-forge,bioconda",
203 "model_class": "CondaDependencyResolver",
204 "prefix": "/home/rkhaled/miniconda3",
205 "read_only": false,
206 "resolver_type": "conda",
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247 "model_class": "CondaDependencyResolver",
248 "prefix": "/home/rkhaled/miniconda3",
249 "read_only": false,
250 "resolver_type": "conda",
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252 "use_local": false,
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269 "model_class": "CondaDependencyResolver",
270 "prefix": "/home/rkhaled/miniconda3",
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290 "ensure_channels": "conda-forge,bioconda",
291 "model_class": "CondaDependencyResolver",
292 "prefix": "/home/rkhaled/miniconda3",
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312 "ensure_channels": "conda-forge,bioconda",
313 "model_class": "CondaDependencyResolver",
314 "prefix": "/home/rkhaled/miniconda3",
315 "read_only": false,
316 "resolver_type": "conda",
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334 "ensure_channels": "conda-forge,bioconda",
335 "model_class": "CondaDependencyResolver",
336 "prefix": "/home/rkhaled/miniconda3",
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343 "dependency_type": "conda",
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356 "ensure_channels": "conda-forge,bioconda",
357 "model_class": "CondaDependencyResolver",
358 "prefix": "/home/rkhaled/miniconda3",
359 "read_only": false,
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367 "exact": true,
368 "model_class": "MergedCondaDependency",
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372 {
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378 "ensure_channels": "conda-forge,bioconda",
379 "model_class": "CondaDependencyResolver",
380 "prefix": "/home/rkhaled/miniconda3",
381 "read_only": false,
382 "resolver_type": "conda",
383 "resolves_simple_dependencies": true,
384 "use_local": false,
385 "versionless": false
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387 "dependency_type": "conda",
388 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-bdd4a85f8bf182a44b33909cd353bfe9976ca4f7cd7e03cfde43ddec0191410c",
389 "exact": true,
390 "model_class": "MergedCondaDependency",
391 "name": "dna_features_viewer",
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394 ],
395 "exit_code": 0,
396 "external_id": "152624",
397 "galaxy_version": "24.2",
398 "handler": null,
399 "history_id": "723c01d174904c31",
400 "id": "297141c205679f60",
401 "inputs": {
402 "domestication_csv": {
403 "id": "0712ecd128ea57d7",
404 "src": "hda",
405 "uuid": "62b232e6-6915-467a-9e55-febd6b17d9d7"
406 },
407 "genbank_files": {
408 "id": "4e411fc6241b00c0",
409 "src": "hda",
410 "uuid": "bff36fb4-2ddc-497c-a812-b821fcafcaf6"
411 },
412 "genbank_files1": {
413 "id": "4e411fc6241b00c0",
414 "src": "hda",
415 "uuid": "bff36fb4-2ddc-497c-a812-b821fcafcaf6"
416 },
417 "genbank_files2": {
418 "id": "53c1d5da63e22734",
419 "src": "hda",
420 "uuid": "c94619a2-c571-4719-8d77-fe8e5566092f"
421 },
422 "genbank_files3": {
423 "id": "918757d2d9059ecb",
424 "src": "hda",
425 "uuid": "a8edcb78-9ec5-45f1-b05f-17b619e372a7"
426 },
427 "genbank_files4": {
428 "id": "3d0b1ede0f9f407d",
429 "src": "hda",
430 "uuid": "bc62ddd0-de10-42c4-9aa4-c62010af835d"
431 },
432 "genbank_files5": {
433 "id": "d67f207c70f90bba",
434 "src": "hda",
435 "uuid": "55aa74b8-36ca-474d-ac73-bda39d9e5e01"
436 },
437 "genbank_files6": {
438 "id": "5c88b35f288963f6",
439 "src": "hda",
440 "uuid": "7098d987-4200-4111-9508-bbe109fec271"
441 },
442 "genbank_files7": {
443 "id": "3e3b5a8a813595d7",
444 "src": "hda",
445 "uuid": "781da4ba-2cb5-4cc3-aebb-e066475dfaef"
446 }
447 },
448 "job_messages": [],
449 "job_metrics": [],
450 "job_runner_name": null,
451 "job_stderr": "",
452 "job_stdout": "",
453 "model_class": "Job",
454 "output_collections": {
455 "methprot_gb": {
456 "id": "f16125b2a7e364b6",
457 "src": "hdca"
458 }
459 },
460 "outputs": {
461 "__new_primary_file_methprot_gb|p14_CMVp__": {
462 "id": "85982e889452a524",
463 "src": "hda",
464 "uuid": "4a810eb2-bc3c-4905-8f07-90f63a0b221f"
465 },
466 "__new_primary_file_methprot_gb|p16_bGHpolyA__": {
467 "id": "df7e9e960b92dcd6",
468 "src": "hda",
469 "uuid": "7e5476ac-38cd-4a82-98ad-0fc2222e49df"
470 },
471 "__new_primary_file_methprot_gb|p18_CMVp__": {
472 "id": "ff4a37beb4d084ef",
473 "src": "hda",
474 "uuid": "c8b8371f-c832-4287-8493-a58191a6dafc"
475 },
476 "__new_primary_file_methprot_gb|p19_mNeoGreen__": {
477 "id": "72bf0a10e7ee2b0b",
478 "src": "hda",
479 "uuid": "cb0cb9ab-3856-4998-80d8-c790704d0ea6"
480 },
481 "__new_primary_file_methprot_gb|p22_PGKpolyA__": {
482 "id": "24c3dd01ebb16d97",
483 "src": "hda",
484 "uuid": "08cbae4f-3b7c-4443-b181-b53764c22971"
485 },
486 "__new_primary_file_methprot_gb|p3_2_CAG__": {
487 "id": "93cd9bd35f8d4a08",
488 "src": "hda",
489 "uuid": "d2ff7a41-e0f9-4bea-bc4c-cc7ff6f22836"
490 },
491 "__new_primary_file_methprot_gb|p7_gfp_sequence__": {
492 "id": "78c1a7160169fd44",
493 "src": "hda",
494 "uuid": "6c4d9b0d-486a-4c36-9670-e2266d5a9622"
495 },
496 "output_zip": {
497 "id": "297141c205679f60",
498 "src": "hda",
499 "uuid": "8986a1c0-102c-469b-b20d-012bfab02e3a"
500 }
501 },
502 "params": {
503 "__input_ext": "\"input\"",
504 "adv": "{\"allow_edits\": true, \"use_file_names_as_ids\": true}",
505 "chromInfo": "\"/tmp/tmpbjg5_060/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
506 "dbkey": "\"?\"",
507 "methylation_protection": "true"
508 },
509 "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",
511 "stdout": "Part names were not truncated\n",
512 "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",
514 "tool_stdout": "Part names were not truncated\n",
515 "update_time": "2025-05-12T10:20:09.457096",
516 "user_email": "planemo@galaxyproject.org",
517 "user_id": "f16125b2a7e364b6"
518 },
519 "status": "success",
520 "test_index": 1,
521 "time_seconds": 34.99931049346924,
522 "tool_id": "domestication",
523 "tool_version": "0.1.0+galaxy0"
524 },
525 "has_data": true,
526 "id": "domestication-1"
527 }
528 ],
529 "version": "0.1"
530 }