--- a/output.json	Fri May 23 08:51:50 2025 +0000
+++ b/output.json	Mon Jun 02 09:48:14 2025 +0000
@@ -9,53 +9,57 @@
         {
             "data": {
                 "inputs": {
-                    "annotation_column": "annotation",
-                    "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
-                    "fragment_column": "fragment",
+                    "adv|json_conf": {
+                        "id": "1895a93fdf3c72e9",
+                        "src": "hda"
+                    },
                     "genbank_files": {
-                        "id": "aaa4852d508c750d",
+                        "id": "c0d7a43ba58f94b5",
                         "src": "hdca"
-                    },
-                    "sequence_column": "sequence",
-                    "table": "sample"
+                    }
                 },
                 "job": {
-                    "command_line": "python '/home/rkhaled/galaxytools/tools/save_to_db/save_to_db.py' --input '/tmp/tmp4fafueqc/files/c/4/e/dataset_c4ecd213-c62a-48fe-bfd4-f2eb1c1c6439.dat,/tmp/tmp4fafueqc/files/d/2/d/dataset_d2d9d592-9f6a-488b-b911-e2c122dc898f.dat,/tmp/tmp4fafueqc/files/3/7/a/dataset_37a5bcbb-3cf1-45ae-a439-588268402c0b.dat,/tmp/tmp4fafueqc/files/9/d/d/dataset_9dd9b73e-eb2c-460a-b612-86cc1f86f9b6.dat,/tmp/tmp4fafueqc/files/e/7/e/dataset_e7e7bd21-36d3-4e84-9177-2451bfcc09e7.dat' --sequence_column 'sequence' --annotation_column 'annotation' --db_uri 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db' --table 'sample' --fragment_column 'fragment' --output '/tmp/tmp4fafueqc/job_working_directory/000/6/outputs/dataset_fdf114e7-4317-491d-8e29-85accf371db7.dat' --file_name_mapping '/tmp/tmp4fafueqc/files/c/4/e/dataset_c4ecd213-c62a-48fe-bfd4-f2eb1c1c6439.dat:p7_L7Ae-Weiss.gb,/tmp/tmp4fafueqc/files/d/2/d/dataset_d2d9d592-9f6a-488b-b911-e2c122dc898f.dat:p6_Nt-IgKLsequence.gb,/tmp/tmp4fafueqc/files/3/7/a/dataset_37a5bcbb-3cf1-45ae-a439-588268402c0b.dat:p6_Kozak-ATG.gb,/tmp/tmp4fafueqc/files/9/d/d/dataset_9dd9b73e-eb2c-460a-b612-86cc1f86f9b6.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmp4fafueqc/files/e/7/e/dataset_e7e7bd21-36d3-4e84-9177-2451bfcc09e7.dat:HC_Amp_ccdB.gb'",
+                    "command_line": "python '/home/rkhaled/galaxytools/tools/save_to_db/save_to_db.py' --input '/tmp/tmpxct9x70x/files/3/0/f/dataset_30fc2017-6620-4a80-a60e-0c795c89f106.dat,/tmp/tmpxct9x70x/files/b/f/b/dataset_bfb54321-8ad0-4e42-b307-f32e47e0618a.dat,/tmp/tmpxct9x70x/files/1/e/5/dataset_1e5a0d80-dc9e-42d0-b0e1-c2e78aff18d3.dat,/tmp/tmpxct9x70x/files/a/b/a/dataset_aba8d5b4-a4f3-4487-803c-be5dee1445cd.dat,/tmp/tmpxct9x70x/files/7/b/7/dataset_7b7fb70f-da0c-45e7-ba4e-0e8cb8d31968.dat' --sequence_column '' --annotation_column '' --db_uri '' --table '' --fragment_column '' --output '/tmp/tmpxct9x70x/job_working_directory/000/7/outputs/dataset_41b844ab-5a85-46cd-8367-7ad1fbee7d3c.dat' --file_name_mapping '/tmp/tmpxct9x70x/files/3/0/f/dataset_30fc2017-6620-4a80-a60e-0c795c89f106.dat:p7_L7Ae-Weiss.gb,/tmp/tmpxct9x70x/files/b/f/b/dataset_bfb54321-8ad0-4e42-b307-f32e47e0618a.dat:p6_Nt-IgKLsequence.gb,/tmp/tmpxct9x70x/files/1/e/5/dataset_1e5a0d80-dc9e-42d0-b0e1-c2e78aff18d3.dat:p6_Kozak-ATG.gb,/tmp/tmpxct9x70x/files/a/b/a/dataset_aba8d5b4-a4f3-4487-803c-be5dee1445cd.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmpxct9x70x/files/7/b/7/dataset_7b7fb70f-da0c-45e7-ba4e-0e8cb8d31968.dat:HC_Amp_ccdB.gb' --json_conf '/tmp/tmpxct9x70x/files/f/4/f/dataset_f4fd59e8-f8d6-4be2-8b00-9e12ca8319ef.dat'",
                     "command_version": "",
                     "copied_from_job_id": null,
-                    "create_time": "2025-05-23T08:51:13.261313",
+                    "create_time": "2025-06-02T09:46:35.368351",
                     "dependencies": [],
                     "exit_code": 0,
-                    "external_id": "53981",
+                    "external_id": "129989",
                     "galaxy_version": "24.2",
                     "handler": null,
-                    "history_id": "aaa4852d508c750d",
-                    "id": "42220a2e87c70ae5",
+                    "history_id": "c0d7a43ba58f94b5",
+                    "id": "92e9df4c7abf24ab",
                     "inputs": {
+                        "adv|json_conf": {
+                            "id": "1895a93fdf3c72e9",
+                            "src": "hda",
+                            "uuid": "f4fd59e8-f8d6-4be2-8b00-9e12ca8319ef"
+                        },
                         "genbank_files1": {
-                            "id": "aaa4852d508c750d",
+                            "id": "c0d7a43ba58f94b5",
                             "src": "hda",
-                            "uuid": "c4ecd213-c62a-48fe-bfd4-f2eb1c1c6439"
+                            "uuid": "30fc2017-6620-4a80-a60e-0c795c89f106"
                         },
                         "genbank_files2": {
-                            "id": "6139eb08ad8af00a",
+                            "id": "1e3e46a5cbeec338",
                             "src": "hda",
-                            "uuid": "d2d9d592-9f6a-488b-b911-e2c122dc898f"
+                            "uuid": "bfb54321-8ad0-4e42-b307-f32e47e0618a"
                         },
                         "genbank_files3": {
-                            "id": "cda565c89999ccf5",
+                            "id": "81fab13a93a3da95",
                             "src": "hda",
-                            "uuid": "37a5bcbb-3cf1-45ae-a439-588268402c0b"
+                            "uuid": "1e5a0d80-dc9e-42d0-b0e1-c2e78aff18d3"
                         },
                         "genbank_files4": {
-                            "id": "f072bab19666d9bc",
+                            "id": "a9ff23755d49e4b6",
                             "src": "hda",
-                            "uuid": "9dd9b73e-eb2c-460a-b612-86cc1f86f9b6"
+                            "uuid": "aba8d5b4-a4f3-4487-803c-be5dee1445cd"
                         },
                         "genbank_files5": {
-                            "id": "ede1fe394bce0b73",
+                            "id": "2ca788c708559c16",
                             "src": "hda",
-                            "uuid": "e7e7bd21-36d3-4e84-9177-2451bfcc09e7"
+                            "uuid": "7b7fb70f-da0c-45e7-ba4e-0e8cb8d31968"
                         }
                     },
                     "job_messages": [],
@@ -67,35 +71,36 @@
                     "output_collections": {},
                     "outputs": {
                         "output": {
-                            "id": "42220a2e87c70ae5",
+                            "id": "92e9df4c7abf24ab",
                             "src": "hda",
-                            "uuid": "fdf114e7-4317-491d-8e29-85accf371db7"
+                            "uuid": "41b844ab-5a85-46cd-8367-7ad1fbee7d3c"
                         }
                     },
                     "params": {
                         "__input_ext": "\"input\"",
-                        "annotation_column": "\"annotation\"",
-                        "chromInfo": "\"/tmp/tmp4fafueqc/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
-                        "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"",
+                        "adv": "{\"json_conf\": {\"values\": [{\"id\": 6, \"src\": \"hda\"}]}}",
+                        "annotation_column": null,
+                        "chromInfo": "\"/tmp/tmpxct9x70x/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+                        "db_uri": null,
                         "dbkey": "\"?\"",
-                        "fragment_column": "\"fragment\"",
+                        "fragment_column": null,
                         "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}",
-                        "sequence_column": "\"sequence\"",
-                        "table": "\"sample\""
+                        "sequence_column": null,
+                        "table": null
                     },
                     "state": "ok",
                     "stderr": "",
-                    "stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_c4ecd213-c62a-48fe-bfd4-f2eb1c1c6439.dat\nProcessing file: dataset_d2d9d592-9f6a-488b-b911-e2c122dc898f.dat\nProcessing file: dataset_37a5bcbb-3cf1-45ae-a439-588268402c0b.dat\nProcessing file: dataset_9dd9b73e-eb2c-460a-b612-86cc1f86f9b6.dat\nProcessing file: dataset_e7e7bd21-36d3-4e84-9177-2451bfcc09e7.dat\nInserted 5 fragments.\nFragment names written to '/tmp/tmp4fafueqc/job_working_directory/000/6/outputs/dataset_fdf114e7-4317-491d-8e29-85accf371db7.dat'.\n",
+                    "stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_30fc2017-6620-4a80-a60e-0c795c89f106.dat\nProcessing file: dataset_bfb54321-8ad0-4e42-b307-f32e47e0618a.dat\nProcessing file: dataset_1e5a0d80-dc9e-42d0-b0e1-c2e78aff18d3.dat\nProcessing file: dataset_aba8d5b4-a4f3-4487-803c-be5dee1445cd.dat\nProcessing file: dataset_7b7fb70f-da0c-45e7-ba4e-0e8cb8d31968.dat\nInserted 5 fragments.\nFragment names written to '/tmp/tmpxct9x70x/job_working_directory/000/7/outputs/dataset_41b844ab-5a85-46cd-8367-7ad1fbee7d3c.dat'.\n",
                     "tool_id": "save_to_db",
                     "tool_stderr": "",
-                    "tool_stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_c4ecd213-c62a-48fe-bfd4-f2eb1c1c6439.dat\nProcessing file: dataset_d2d9d592-9f6a-488b-b911-e2c122dc898f.dat\nProcessing file: dataset_37a5bcbb-3cf1-45ae-a439-588268402c0b.dat\nProcessing file: dataset_9dd9b73e-eb2c-460a-b612-86cc1f86f9b6.dat\nProcessing file: dataset_e7e7bd21-36d3-4e84-9177-2451bfcc09e7.dat\nInserted 5 fragments.\nFragment names written to '/tmp/tmp4fafueqc/job_working_directory/000/6/outputs/dataset_fdf114e7-4317-491d-8e29-85accf371db7.dat'.\n",
-                    "update_time": "2025-05-23T08:51:20.615309",
+                    "tool_stdout": "Container 'test_fragments_db' is already running.\nConnected to database.\nProcessing file: dataset_30fc2017-6620-4a80-a60e-0c795c89f106.dat\nProcessing file: dataset_bfb54321-8ad0-4e42-b307-f32e47e0618a.dat\nProcessing file: dataset_1e5a0d80-dc9e-42d0-b0e1-c2e78aff18d3.dat\nProcessing file: dataset_aba8d5b4-a4f3-4487-803c-be5dee1445cd.dat\nProcessing file: dataset_7b7fb70f-da0c-45e7-ba4e-0e8cb8d31968.dat\nInserted 5 fragments.\nFragment names written to '/tmp/tmpxct9x70x/job_working_directory/000/7/outputs/dataset_41b844ab-5a85-46cd-8367-7ad1fbee7d3c.dat'.\n",
+                    "update_time": "2025-06-02T09:46:41.929779",
                     "user_email": "planemo@galaxyproject.org",
-                    "user_id": "aaa4852d508c750d"
+                    "user_id": "c0d7a43ba58f94b5"
                 },
                 "status": "success",
                 "test_index": 0,
-                "time_seconds": 28.753373384475708,
+                "time_seconds": 29.02011752128601,
                 "tool_id": "save_to_db",
                 "tool_version": "0.1.0+galaxy1"
             },