# HG changeset patch
# User tduigou
# Date 1756908434 0
# Node ID 3bb9bbecae97545d2b2a239e62cb01aee78424c9
# Parent 54e716c11b71c5cca304e276d4cc76bb8fdda268
planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 767392e3136912fa30d1e0786eba789dd77d722c-dirty
diff -r 54e716c11b71 -r 3bb9bbecae97 get_db_info.py
--- a/get_db_info.py Tue Jul 29 12:01:32 2025 +0000
+++ b/get_db_info.py Wed Sep 03 14:07:14 2025 +0000
@@ -134,11 +134,10 @@
# Write report file
with open(output_report, "w") as report_file:
if missing_fragments:
- report_file.write("Missing fragment in DB:\n")
for frag in missing_fragments:
report_file.write(f"{frag}\n")
else:
- report_file.write("NO missing fragments in DB\n")
+ report_file.write("")
# === CONTINUE WITH GB FILE CREATION ===
for _, row in df.iterrows():
diff -r 54e716c11b71 -r 3bb9bbecae97 output.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/output.html Wed Sep 03 14:07:14 2025 +0000
@@ -0,0 +1,291 @@
+
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+ Test Results (powered by Planemo)
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\ No newline at end of file
diff -r 54e716c11b71 -r 3bb9bbecae97 output.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/output.json Wed Sep 03 14:07:14 2025 +0000
@@ -0,0 +1,604 @@
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+ "output_gb": {
+ "id": "692a3006cb4bc1fb",
+ "src": "hdca"
+ }
+ },
+ "outputs": {
+ "__new_primary_file_output_gb|part_A__": {
+ "id": "9b676d2a6fac5122",
+ "src": "hda",
+ "uuid": "e4cbafe5-d29f-423a-8d0f-6251c8a1b861"
+ },
+ "__new_primary_file_output_gb|part_B__": {
+ "id": "6408e022581bd85a",
+ "src": "hda",
+ "uuid": "d6a1ef9b-5407-4166-8b2d-dc9add921f8d"
+ },
+ "__new_primary_file_output_gb|part_C__": {
+ "id": "146b9743658be563",
+ "src": "hda",
+ "uuid": "1d58408c-1c4d-4b13-8e60-7551bb2d033e"
+ },
+ "__new_primary_file_output_gb|part_D__": {
+ "id": "d04b3965e2c7c627",
+ "src": "hda",
+ "uuid": "277c9e3f-b008-47f9-9c27-feded9a8c000"
+ },
+ "__new_primary_file_output_gb|part_E__": {
+ "id": "5171793c10a10766",
+ "src": "hda",
+ "uuid": "80e12f72-1dc8-4b72-b93f-bb899aedb134"
+ },
+ "__new_primary_file_output_gb|part_F__": {
+ "id": "4a9fd232cf6f8097",
+ "src": "hda",
+ "uuid": "f8f33f16-72d1-43cb-9b59-9591026646f2"
+ },
+ "__new_primary_file_output_gb|part_G__": {
+ "id": "74e6cbe048c63d70",
+ "src": "hda",
+ "uuid": "c0acfcfd-504c-434a-b9f9-6d6683dd5c3c"
+ },
+ "__new_primary_file_output_gb|part_H__": {
+ "id": "ca3637e630bf95c2",
+ "src": "hda",
+ "uuid": "01803f35-1b7f-44f5-bf0e-ff133082eb1f"
+ },
+ "__new_primary_file_output_gb|part_I__": {
+ "id": "8c369d98999df6bc",
+ "src": "hda",
+ "uuid": "df4b8de1-4e8f-467a-8361-567b4d53dbcc"
+ },
+ "__new_primary_file_output_gb|part_J__": {
+ "id": "0ba9e9781a802f97",
+ "src": "hda",
+ "uuid": "d054d23e-5d67-4ec2-a0cf-5bb61a7693be"
+ },
+ "__new_primary_file_output_gb|part_K__": {
+ "id": "1cd3d77f4e0bb87b",
+ "src": "hda",
+ "uuid": "a3dbb7ee-3c64-49b4-b024-e92178c9c52b"
+ },
+ "__new_primary_file_output_gb|part_L__": {
+ "id": "fc7f2bf0d5edf8ad",
+ "src": "hda",
+ "uuid": "cb4b9a89-166d-4d35-9b20-6e06c71ff3fc"
+ },
+ "report": {
+ "id": "cc9ee5a2b3669654",
+ "src": "hda",
+ "uuid": "2099de02-84b6-464f-a603-26ec7fd84555"
+ }
+ },
+ "params": {
+ "__input_ext": "\"input\"",
+ "chromInfo": "\"/tmp/tmpk1dzvi78/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+ "dbkey": "\"?\"",
+ "json_use": "{\"__current_case__\": 0, \"annotation_columns\": \"annotation\", \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\", \"fragment_column\": \"fragment\", \"sequence_column\": \"sequence\", \"table\": \"sample\", \"use_json_paramers\": false}"
+ },
+ "state": "ok",
+ "stderr": "",
+ "stdout": "Connected to database.\n",
+ "tool_id": "seq_form_db",
+ "tool_stderr": "",
+ "tool_stdout": "Connected to database.\n",
+ "update_time": "2025-09-03T14:06:41.527586",
+ "user_email": "planemo@galaxyproject.org",
+ "user_id": "4a322b718ac1c0e2"
+ },
+ "status": "success",
+ "test_index": 2,
+ "time_seconds": 16.304288148880005,
+ "tool_id": "seq_form_db",
+ "tool_version": "0.3.0+galaxy2"
+ },
+ "has_data": true,
+ "id": "seq_form_db-2"
+ }
+ ],
+ "version": "0.1"
+}
\ No newline at end of file
diff -r 54e716c11b71 -r 3bb9bbecae97 seq_form_db.xml
--- a/seq_form_db.xml Tue Jul 29 12:01:32 2025 +0000
+++ b/seq_form_db.xml Wed Sep 03 14:07:14 2025 +0000
@@ -1,8 +1,8 @@
Import fragment's data from an accessible DB and export it as .gb files
- 2
- 0.3.0
+ 3
+ 0.3.1
pandas
@@ -47,7 +47,7 @@
-
+
@@ -125,8 +125,7 @@
@@ -201,8 +200,7 @@
@@ -281,8 +279,7 @@