Mercurial > repos > tduigou > save_to_db

annotate output.json @ 5:f934215bdb78 draft default tip

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planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Mon, 02 Jun 2025 10:29:28 +0000
parents c7a7520afb4b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents:
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1 {
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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2 "summary": {
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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3 "num_errors": 0,
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f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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4 "num_failures": 1,
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034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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5 "num_skips": 0,
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f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
parents: 4
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6 "num_tests": 2
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034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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7 },
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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8 "tests": [
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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9 {
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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10 "data": {
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11 "inputs": {
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12 "adv|json_conf": {
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13 "id": "c9e99bc7539b08e5",
4
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14 "src": "hda"
c7a7520afb4b planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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15 },
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eca0d710bbe9 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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16 "genbank_files": {
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f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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17 "id": "c804608f95de6282",
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eca0d710bbe9 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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18 "src": "hdca"
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c7a7520afb4b planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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19 }
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034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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20 },
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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21 "job": {
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f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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22 "command_line": "python '/home/rkhaled/galaxytools/tools/save_to_db/save_to_db.py' --input '/tmp/tmpgfe8mdmw/files/a/5/a/dataset_a5a56a5c-573a-4b34-8c98-27b2edff54f3.dat,/tmp/tmpgfe8mdmw/files/1/7/7/dataset_1779bfb3-ff31-4b6d-8c6f-82172c987fee.dat,/tmp/tmpgfe8mdmw/files/4/c/c/dataset_4cc83056-e7b7-4dcd-9360-cde2bc1978f1.dat,/tmp/tmpgfe8mdmw/files/9/6/9/dataset_969b7b35-4f05-48bc-92f5-4e2f5ce375ca.dat,/tmp/tmpgfe8mdmw/files/7/b/4/dataset_7b47f46b-3e00-4a65-9c9a-6a25e3c30b04.dat' --sequence_column '' --annotation_column '' --db_uri '' --table '' --fragment_column '' --output '/tmp/tmpgfe8mdmw/job_working_directory/000/7/outputs/dataset_89f2f3f4-04a0-4998-a3f6-d065b9e1f365.dat' --file_name_mapping '/tmp/tmpgfe8mdmw/files/a/5/a/dataset_a5a56a5c-573a-4b34-8c98-27b2edff54f3.dat:p7_L7Ae-Weiss.gb,/tmp/tmpgfe8mdmw/files/1/7/7/dataset_1779bfb3-ff31-4b6d-8c6f-82172c987fee.dat:p6_Nt-IgKLsequence.gb,/tmp/tmpgfe8mdmw/files/4/c/c/dataset_4cc83056-e7b7-4dcd-9360-cde2bc1978f1.dat:p6_Kozak-ATG.gb,/tmp/tmpgfe8mdmw/files/9/6/9/dataset_969b7b35-4f05-48bc-92f5-4e2f5ce375ca.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmpgfe8mdmw/files/7/b/4/dataset_7b47f46b-3e00-4a65-9c9a-6a25e3c30b04.dat:HC_Amp_ccdB.gb' --json_conf '/tmp/tmpgfe8mdmw/files/b/3/e/dataset_b3e3a95b-dd84-41de-b53b-ea44d034e11b.dat'",
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034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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23 "command_version": "",
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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24 "copied_from_job_id": null,
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f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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25 "create_time": "2025-06-02T10:25:46.744304",
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034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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26 "dependencies": [],
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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27 "exit_code": 0,
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f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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28 "external_id": "148807",
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034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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29 "galaxy_version": "24.2",
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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30 "handler": null,
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f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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31 "history_id": "c804608f95de6282",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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32 "id": "91a273dde5f46de6",
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034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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33 "inputs": {
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34 "adv|json_conf": {
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f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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35 "id": "c9e99bc7539b08e5",
4
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36 "src": "hda",
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f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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37 "uuid": "b3e3a95b-dd84-41de-b53b-ea44d034e11b"
4
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38 },
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39 "genbank_files1": {
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f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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40 "id": "c804608f95de6282",
0
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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41 "src": "hda",
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f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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42 "uuid": "a5a56a5c-573a-4b34-8c98-27b2edff54f3"
0
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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43 },
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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44 "genbank_files2": {
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f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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45 "id": "dc78a71e9d46a610",
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034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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46 "src": "hda",
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47 "uuid": "1779bfb3-ff31-4b6d-8c6f-82172c987fee"
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48 },
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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49 "genbank_files3": {
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f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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50 "id": "32d06e9182be9fe5",
0
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51 "src": "hda",
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52 "uuid": "4cc83056-e7b7-4dcd-9360-cde2bc1978f1"
0
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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53 },
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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54 "genbank_files4": {
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55 "id": "a50e356be1f2db6f",
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56 "src": "hda",
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f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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57 "uuid": "969b7b35-4f05-48bc-92f5-4e2f5ce375ca"
0
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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58 },
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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59 "genbank_files5": {
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60 "id": "64d80998680b05e1",
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61 "src": "hda",
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62 "uuid": "7b47f46b-3e00-4a65-9c9a-6a25e3c30b04"
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63 }
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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64 },
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65 "job_messages": [],
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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66 "job_metrics": [],
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67 "job_runner_name": null,
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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68 "job_stderr": "",
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69 "job_stdout": "",
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70 "model_class": "Job",
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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71 "output_collections": {},
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72 "outputs": {
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73 "output": {
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74 "id": "91a273dde5f46de6",
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75 "src": "hda",
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76 "uuid": "89f2f3f4-04a0-4998-a3f6-d065b9e1f365"
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77 }
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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78 },
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79 "params": {
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80 "__input_ext": "\"input\"",
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81 "adv": "{\"json_conf\": {\"values\": [{\"id\": 6, \"src\": \"hda\"}]}}",
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82 "annotation_column": null,
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83 "chromInfo": "\"/tmp/tmpgfe8mdmw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
4
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84 "db_uri": null,
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85 "dbkey": "\"?\"",
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86 "fragment_column": null,
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eca0d710bbe9 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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87 "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}",
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88 "sequence_column": null,
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89 "table": null
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90 },
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91 "state": "ok",
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92 "stderr": "",
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93 "stdout": "Execution was blocked by config (execution = false)\n",
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94 "tool_id": "save_to_db",
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95 "tool_stderr": "",
5
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96 "tool_stdout": "Execution was blocked by config (execution = false)\n",
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97 "update_time": "2025-06-02T10:25:54.228017",
0
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98 "user_email": "planemo@galaxyproject.org",
5
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99 "user_id": "c804608f95de6282"
0
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100 },
5
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101 "output_problems": [
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102 "Output output: different than expected\nExpected 5+-0 lines in the output found 0"
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103 ],
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104 "status": "failure",
0
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105 "test_index": 0,
5
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106 "time_seconds": 28.49768567085266,
0
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107 "tool_id": "save_to_db",
5
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108 "tool_version": "0.2.0+galaxy2"
0
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109 },
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110 "has_data": true,
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111 "id": "save_to_db-0"
5
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112 },
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113 {
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114 "data": {
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115 "inputs": {
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116 "adv|json_conf": {
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117 "id": "ba5e0bd88cc3030c",
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118 "src": "hda"
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119 },
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120 "genbank_files": {
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121 "id": "dc78a71e9d46a610",
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122 "src": "hdca"
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123 }
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124 },
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125 "job": {
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126 "command_line": "python '/home/rkhaled/galaxytools/tools/save_to_db/save_to_db.py' --input '/tmp/tmpgfe8mdmw/files/3/6/2/dataset_362bcc57-3b7e-4089-b9c7-33155498d352.dat,/tmp/tmpgfe8mdmw/files/4/e/0/dataset_4e03baea-fd7c-45b3-b808-4443adc60f91.dat,/tmp/tmpgfe8mdmw/files/6/d/a/dataset_6da90158-c02d-457e-8908-56b532b4b3c2.dat,/tmp/tmpgfe8mdmw/files/8/0/b/dataset_80b64d26-b0b2-40df-ad9b-41446c172705.dat,/tmp/tmpgfe8mdmw/files/3/8/7/dataset_38751000-4953-44bb-b142-81b4bc41ad97.dat' --sequence_column '' --annotation_column '' --db_uri '' --table '' --fragment_column '' --output '/tmp/tmpgfe8mdmw/job_working_directory/000/14/outputs/dataset_ee43072f-661d-47e0-b30f-d905aac37a4a.dat' --file_name_mapping '/tmp/tmpgfe8mdmw/files/3/6/2/dataset_362bcc57-3b7e-4089-b9c7-33155498d352.dat:p7_L7Ae-Weiss.gb,/tmp/tmpgfe8mdmw/files/4/e/0/dataset_4e03baea-fd7c-45b3-b808-4443adc60f91.dat:p6_Nt-IgKLsequence.gb,/tmp/tmpgfe8mdmw/files/6/d/a/dataset_6da90158-c02d-457e-8908-56b532b4b3c2.dat:p6_Kozak-ATG.gb,/tmp/tmpgfe8mdmw/files/8/0/b/dataset_80b64d26-b0b2-40df-ad9b-41446c172705.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmpgfe8mdmw/files/3/8/7/dataset_38751000-4953-44bb-b142-81b4bc41ad97.dat:HC_Amp_ccdB.gb' --json_conf '/tmp/tmpgfe8mdmw/files/8/3/d/dataset_83ddd986-5a07-406e-91f8-fcc403a6e927.dat'",
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127 "command_version": "",
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128 "copied_from_job_id": null,
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129 "create_time": "2025-06-02T10:26:14.771419",
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130 "dependencies": [
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131 {
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132 "cacheable": false,
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133 "dependency_resolver": {
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134 "auto_init": true,
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135 "auto_install": true,
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136 "can_uninstall_dependencies": true,
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137 "ensure_channels": "conda-forge,bioconda",
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138 "model_class": "CondaDependencyResolver",
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139 "prefix": "/home/rkhaled/miniconda3",
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140 "read_only": false,
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141 "resolver_type": "conda",
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142 "resolves_simple_dependencies": true,
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143 "use_local": false,
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144 "versionless": false
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145 },
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146 "dependency_type": "conda",
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147 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
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148 "exact": true,
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149 "model_class": "MergedCondaDependency",
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150 "name": "pandas",
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151 "version": "2.2.3"
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152 },
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153 {
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154 "cacheable": false,
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155 "dependency_resolver": {
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156 "auto_init": true,
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157 "auto_install": true,
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158 "can_uninstall_dependencies": true,
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159 "ensure_channels": "conda-forge,bioconda",
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160 "model_class": "CondaDependencyResolver",
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161 "prefix": "/home/rkhaled/miniconda3",
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162 "read_only": false,
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163 "resolver_type": "conda",
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164 "resolves_simple_dependencies": true,
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165 "use_local": false,
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166 "versionless": false
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167 },
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168 "dependency_type": "conda",
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169 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
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170 "exact": true,
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171 "model_class": "MergedCondaDependency",
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172 "name": "sqlalchemy",
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173 "version": "2.0.40"
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174 },
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175 {
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176 "cacheable": false,
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177 "dependency_resolver": {
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178 "auto_init": true,
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179 "auto_install": true,
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180 "can_uninstall_dependencies": true,
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181 "ensure_channels": "conda-forge,bioconda",
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182 "model_class": "CondaDependencyResolver",
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183 "prefix": "/home/rkhaled/miniconda3",
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184 "read_only": false,
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185 "resolver_type": "conda",
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186 "resolves_simple_dependencies": true,
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187 "use_local": false,
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188 "versionless": false
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189 },
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190 "dependency_type": "conda",
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191 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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diff changeset
192 "exact": true,
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193 "model_class": "MergedCondaDependency",
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194 "name": "psycopg2",
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195 "version": "2.9.9"
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196 }
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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197 ],
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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diff changeset
198 "exit_code": 0,
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199 "external_id": "149308",
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200 "galaxy_version": "24.2",
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diff changeset
201 "handler": null,
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202 "history_id": "dc78a71e9d46a610",
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diff changeset
203 "id": "c6ad8bbeb64086ff",
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diff changeset
204 "inputs": {
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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205 "adv|json_conf": {
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206 "id": "ba5e0bd88cc3030c",
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207 "src": "hda",
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208 "uuid": "83ddd986-5a07-406e-91f8-fcc403a6e927"
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209 },
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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210 "genbank_files1": {
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211 "id": "4da6c37b755c621f",
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212 "src": "hda",
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213 "uuid": "362bcc57-3b7e-4089-b9c7-33155498d352"
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214 },
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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215 "genbank_files2": {
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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216 "id": "83933cf19817c19f",
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217 "src": "hda",
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218 "uuid": "4e03baea-fd7c-45b3-b808-4443adc60f91"
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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219 },
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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220 "genbank_files3": {
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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221 "id": "33ff3c6dc742881e",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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222 "src": "hda",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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223 "uuid": "6da90158-c02d-457e-8908-56b532b4b3c2"
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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224 },
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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225 "genbank_files4": {
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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226 "id": "8187d0d2b67e72bf",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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227 "src": "hda",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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228 "uuid": "80b64d26-b0b2-40df-ad9b-41446c172705"
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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229 },
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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230 "genbank_files5": {
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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231 "id": "a744ea399046e427",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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232 "src": "hda",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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233 "uuid": "38751000-4953-44bb-b142-81b4bc41ad97"
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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234 }
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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235 },
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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236 "job_messages": [],
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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237 "job_metrics": [],
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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238 "job_runner_name": null,
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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239 "job_stderr": "",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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240 "job_stdout": "",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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241 "model_class": "Job",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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242 "output_collections": {},
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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243 "outputs": {
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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244 "output": {
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245 "id": "c6ad8bbeb64086ff",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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246 "src": "hda",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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247 "uuid": "ee43072f-661d-47e0-b30f-d905aac37a4a"
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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248 }
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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249 },
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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parents: 4
diff changeset
250 "params": {
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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251 "__input_ext": "\"input\"",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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252 "adv": "{\"json_conf\": {\"values\": [{\"id\": 13, \"src\": \"hda\"}]}}",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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253 "annotation_column": null,
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254 "chromInfo": "\"/tmp/tmpgfe8mdmw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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255 "db_uri": null,
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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diff changeset
256 "dbkey": "\"?\"",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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diff changeset
257 "fragment_column": null,
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258 "genbank_files": "{\"values\": [{\"id\": 2, \"src\": \"hdca\"}]}",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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diff changeset
259 "sequence_column": null,
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260 "table": null
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261 },
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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262 "state": "ok",
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263 "stderr": "",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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264 "stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_362bcc57-3b7e-4089-b9c7-33155498d352.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_4e03baea-fd7c-45b3-b808-4443adc60f91.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_6da90158-c02d-457e-8908-56b532b4b3c2.dat(p6_Kozak-ATG)\nProcessing file: dataset_80b64d26-b0b2-40df-ad9b-41446c172705.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_38751000-4953-44bb-b142-81b4bc41ad97.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmpgfe8mdmw/job_working_directory/000/14/outputs/dataset_ee43072f-661d-47e0-b30f-d905aac37a4a.dat'.\n",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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265 "tool_id": "save_to_db",
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266 "tool_stderr": "",
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267 "tool_stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_362bcc57-3b7e-4089-b9c7-33155498d352.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_4e03baea-fd7c-45b3-b808-4443adc60f91.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_6da90158-c02d-457e-8908-56b532b4b3c2.dat(p6_Kozak-ATG)\nProcessing file: dataset_80b64d26-b0b2-40df-ad9b-41446c172705.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_38751000-4953-44bb-b142-81b4bc41ad97.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmpgfe8mdmw/job_working_directory/000/14/outputs/dataset_ee43072f-661d-47e0-b30f-d905aac37a4a.dat'.\n",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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268 "update_time": "2025-06-02T10:26:21.180586",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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diff changeset
269 "user_email": "planemo@galaxyproject.org",
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diff changeset
270 "user_id": "c804608f95de6282"
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diff changeset
271 },
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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diff changeset
272 "status": "success",
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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parents: 4
diff changeset
273 "test_index": 1,
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diff changeset
274 "time_seconds": 26.70093870162964,
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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diff changeset
275 "tool_id": "save_to_db",
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diff changeset
276 "tool_version": "0.2.0+galaxy2"
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diff changeset
277 },
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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parents: 4
diff changeset
278 "has_data": true,
f934215bdb78 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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diff changeset
279 "id": "save_to_db-1"
0
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parents:
diff changeset
280 }
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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parents:
diff changeset
281 ],
034686b5bc15 planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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parents:
diff changeset
282 "version": "0.1"
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283 }