Mercurial > repos > tduigou > parameters_maystro

annotate output.json @ 0:1a766d8d3883 draft

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author tduigou
date Fri, 11 Jul 2025 10:10:16 +0000
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children 34135dac85b0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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1 {
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2 "summary": {
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3 "num_errors": 0,
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4 "num_failures": 0,
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5 "num_skips": 0,
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6 "num_tests": 2
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7 },
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8 "tests": [
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9 {
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10 "data": {
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11 "inputs": {
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12 "distribute_json": false,
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13 "json_from_workflow": [
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14 {
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15 "id": "051ed7ff50845d8c",
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16 "src": "hda"
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17 },
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18 {
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19 "id": "25656ddfec77a3b3",
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20 "src": "hda"
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21 }
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22 ]
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23 },
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24 "job": {
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25 "command_line": "python '/home/rkhaled/galaxytools/tools/parameters_maystro/maystro.py' --distribute_json 'false' --json_from_workflow \"/tmp/tmpfpd6tei1/files/2/f/4/dataset_2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6.dat\" \"/tmp/tmpfpd6tei1/files/9/6/0/dataset_960eac8e-fb66-4982-8009-4896c9e57b38.dat\" --json_from_user 'None' --json_name_mapping /tmp/tmpfpd6tei1/files/2/f/4/dataset_2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6.dat:seq_from_db_param.json,/tmp/tmpfpd6tei1/files/9/6/0/dataset_960eac8e-fb66-4982-8009-4896c9e57b38.dat:seq_to_db_param.json --output_workflow '/tmp/tmpfpd6tei1/job_working_directory/000/3/outputs/dataset_d100f4ee-f845-4a68-be68-004c7af9679d.dat' --output_user '/tmp/tmpfpd6tei1/job_working_directory/000/3/outputs/dataset_1e2a9024-ad29-4d18-b95d-645817393383.dat' && echo 'DEBUB' && cat '/tmp/tmpfpd6tei1/job_working_directory/000/3/outputs/dataset_1e2a9024-ad29-4d18-b95d-645817393383.dat'",
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26 "command_version": "",
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27 "copied_from_job_id": null,
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28 "create_time": "2025-07-11T09:42:39.854743",
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29 "dependencies": [],
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30 "exit_code": 0,
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31 "external_id": "79277",
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32 "galaxy_version": "25.0",
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33 "handler": null,
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34 "history_id": "051ed7ff50845d8c",
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35 "id": "d66447d427a79ce4",
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36 "inputs": {
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37 "json_from_workflow": {
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38 "id": "051ed7ff50845d8c",
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39 "src": "hda",
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40 "uuid": "2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6"
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41 },
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42 "json_from_workflow1": {
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43 "id": "051ed7ff50845d8c",
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44 "src": "hda",
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45 "uuid": "2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6"
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46 },
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47 "json_from_workflow2": {
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48 "id": "25656ddfec77a3b3",
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49 "src": "hda",
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50 "uuid": "960eac8e-fb66-4982-8009-4896c9e57b38"
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51 }
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52 },
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53 "job_messages": [],
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54 "job_metrics": [],
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55 "job_runner_name": null,
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56 "job_stderr": "",
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57 "job_stdout": "",
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58 "model_class": "Job",
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59 "output_collections": {},
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60 "outputs": {
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61 "output_user": {
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62 "id": "39496c7f8d685f43",
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63 "src": "hda",
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64 "uuid": "1e2a9024-ad29-4d18-b95d-645817393383"
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65 },
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66 "output_workflow": {
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67 "id": "d66447d427a79ce4",
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68 "src": "hda",
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69 "uuid": "d100f4ee-f845-4a68-be68-004c7af9679d"
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70 }
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71 },
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72 "params": {
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73 "__input_ext": "\"input\"",
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74 "chromInfo": "\"/tmp/tmpfpd6tei1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
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75 "dbkey": "\"?\"",
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76 "distribute_json": "false",
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77 "json_from_user": null
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78 },
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79 "state": "ok",
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80 "stderr": "",
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81 "stdout": "[INFO] Watching temp dir for new JSONs: /tmp/tmpfpd6tei1/tmp/maystro_merge_xd06s1et\n[INFO] Initial JSONs from workflow: ['/tmp/tmpfpd6tei1/files/2/f/4/dataset_2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6.dat', '/tmp/tmpfpd6tei1/files/9/6/0/dataset_960eac8e-fb66-4982-8009-4896c9e57b38.dat']\n[INFO] Added data under key: seq_from_db_param\n[INFO] Added data under key: seq_to_db_param\n[INFO] Merged JSON written to: /tmp/tmpfpd6tei1/job_working_directory/000/3/outputs/dataset_1e2a9024-ad29-4d18-b95d-645817393383.dat\n[INFO] Cleaning up: /tmp/tmpfpd6tei1/tmp/maystro_merge_xd06s1et\nDEBUB\n{\n \"seq_from_db_param\": {\n \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n },\n \"seq_to_db_param\": {\n \"execution\": true,\n \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n }\n}",
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82 "tool_id": "parameters_maystro",
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83 "tool_stderr": "",
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84 "tool_stdout": "[INFO] Watching temp dir for new JSONs: /tmp/tmpfpd6tei1/tmp/maystro_merge_xd06s1et\n[INFO] Initial JSONs from workflow: ['/tmp/tmpfpd6tei1/files/2/f/4/dataset_2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6.dat', '/tmp/tmpfpd6tei1/files/9/6/0/dataset_960eac8e-fb66-4982-8009-4896c9e57b38.dat']\n[INFO] Added data under key: seq_from_db_param\n[INFO] Added data under key: seq_to_db_param\n[INFO] Merged JSON written to: /tmp/tmpfpd6tei1/job_working_directory/000/3/outputs/dataset_1e2a9024-ad29-4d18-b95d-645817393383.dat\n[INFO] Cleaning up: /tmp/tmpfpd6tei1/tmp/maystro_merge_xd06s1et\nDEBUB\n{\n \"seq_from_db_param\": {\n \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n },\n \"seq_to_db_param\": {\n \"execution\": true,\n \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n }\n}",
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85 "update_time": "2025-07-11T09:42:45.494563",
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86 "user_email": "planemo@galaxyproject.org",
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87 "user_id": "051ed7ff50845d8c"
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88 },
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89 "status": "success",
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90 "test_index": 0,
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91 "time_seconds": 16.301273107528687,
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92 "tool_id": "parameters_maystro",
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93 "tool_version": "0.1.0+galaxy1"
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94 },
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95 "has_data": true,
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96 "id": "parameters_maystro-0"
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97 },
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98 {
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99 "data": {
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100 "inputs": {
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101 "distribute_json": true,
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102 "json_from_user": {
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103 "id": "10ea9be91661a5fd",
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104 "src": "hda"
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105 },
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106 "json_from_workflow": [
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107 {
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108 "id": "b7e19a053756efb9",
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109 "src": "hda"
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110 },
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111 {
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112 "id": "45e8a4dfb17d83f9",
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113 "src": "hda"
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114 }
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115 ]
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116 },
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117 "job": {
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118 "command_line": "python '/home/rkhaled/galaxytools/tools/parameters_maystro/maystro.py' --distribute_json 'true' --json_from_workflow \"/tmp/tmpfpd6tei1/files/c/1/e/dataset_c1e98b32-965c-4a0d-9c7f-26973a7e0fe6.dat\" \"/tmp/tmpfpd6tei1/files/3/a/5/dataset_3a560c20-0d3f-4aae-abd4-4a460698f28f.dat\" --json_from_user '/tmp/tmpfpd6tei1/files/0/a/b/dataset_0abf65a6-bd5b-47fc-94ba-a6a97fa6d88b.dat' --json_name_mapping /tmp/tmpfpd6tei1/files/c/1/e/dataset_c1e98b32-965c-4a0d-9c7f-26973a7e0fe6.dat:seq_from_db_param.json,/tmp/tmpfpd6tei1/files/3/a/5/dataset_3a560c20-0d3f-4aae-abd4-4a460698f28f.dat:seq_to_db_param.json --output_workflow '/tmp/tmpfpd6tei1/job_working_directory/000/7/outputs/dataset_5254084b-4d71-4098-b933-f73a9e7d5a28.dat' --output_user '/tmp/tmpfpd6tei1/job_working_directory/000/7/outputs/dataset_04c60445-2ff4-4b59-bcbc-75f08b68625a.dat' && echo 'DEBUB' && cat '/tmp/tmpfpd6tei1/job_working_directory/000/7/outputs/dataset_04c60445-2ff4-4b59-bcbc-75f08b68625a.dat'",
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119 "command_version": "",
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120 "copied_from_job_id": null,
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121 "create_time": "2025-07-11T09:42:56.883885",
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122 "dependencies": [],
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123 "exit_code": 0,
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124 "external_id": "79598",
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125 "galaxy_version": "25.0",
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126 "handler": null,
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127 "history_id": "25656ddfec77a3b3",
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128 "id": "10ea9be91661a5fd",
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129 "inputs": {
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130 "json_from_user": {
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131 "id": "10ea9be91661a5fd",
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132 "src": "hda",
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133 "uuid": "0abf65a6-bd5b-47fc-94ba-a6a97fa6d88b"
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134 },
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135 "json_from_workflow": {
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136 "id": "b7e19a053756efb9",
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137 "src": "hda",
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138 "uuid": "c1e98b32-965c-4a0d-9c7f-26973a7e0fe6"
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139 },
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140 "json_from_workflow1": {
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141 "id": "b7e19a053756efb9",
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142 "src": "hda",
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143 "uuid": "c1e98b32-965c-4a0d-9c7f-26973a7e0fe6"
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144 },
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145 "json_from_workflow2": {
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146 "id": "45e8a4dfb17d83f9",
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147 "src": "hda",
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148 "uuid": "3a560c20-0d3f-4aae-abd4-4a460698f28f"
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149 }
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150 },
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151 "job_messages": [],
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152 "job_metrics": [],
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153 "job_runner_name": null,
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154 "job_stderr": "",
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155 "job_stdout": "",
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156 "model_class": "Job",
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157 "output_collections": {},
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158 "outputs": {
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159 "output_user": {
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160 "id": "295d652904818249",
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161 "src": "hda",
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162 "uuid": "04c60445-2ff4-4b59-bcbc-75f08b68625a"
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163 },
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164 "output_workflow": {
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165 "id": "8c61ed432685cfe0",
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166 "src": "hda",
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167 "uuid": "5254084b-4d71-4098-b933-f73a9e7d5a28"
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168 }
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169 },
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170 "params": {
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171 "__input_ext": "\"input\"",
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172 "chromInfo": "\"/tmp/tmpfpd6tei1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
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173 "dbkey": "\"?\"",
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174 "distribute_json": "true"
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175 },
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176 "state": "ok",
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177 "stderr": "",
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178 "stdout": "DEBUB\n",
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179 "tool_id": "parameters_maystro",
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180 "tool_stderr": "",
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181 "tool_stdout": "DEBUB\n",
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182 "update_time": "2025-07-11T09:43:02.149865",
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183 "user_email": "planemo@galaxyproject.org",
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184 "user_id": "051ed7ff50845d8c"
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185 },
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186 "status": "success",
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187 "test_index": 1,
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188 "time_seconds": 16.54760479927063,
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189 "tool_id": "parameters_maystro",
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190 "tool_version": "0.1.0+galaxy1"
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191 },
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192 "has_data": true,
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193 "id": "parameters_maystro-1"
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194 }
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195 ],
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196 "version": "0.1"
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197 }