# HG changeset patch # User tduigou # Date 1767699253 0 # Node ID e7ecf6e21b49e4fdda3ce75d47b5abea495d119a # Parent 2655e08cd61af7d43400b4a8588b1e357d3cc1ac planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit e8c8f102cab10531ed588be4ecb8a0d01e797f09 diff -r 2655e08cd61a -r e7ecf6e21b49 cloning_similation.xml --- a/cloning_similation.xml Wed Jul 23 09:46:59 2025 +0000 +++ b/cloning_similation.xml Tue Jan 06 11:34:13 2026 +0000 @@ -1,7 +1,7 @@ A cloning simulator for synthetic biology - 1 + 2 0.2.0 @@ -34,7 +34,7 @@ --file_name_mapping '$file_name_mapping' --file_name_mapping_dom '$file_name_mapping_dom' --use_json_paramers '$json_use.use_json_paramers' - #if not $json_use.use_json_paramers: + #if $json_use.use_json_paramers=='false': --enzyme '$json_use.enzyme' --topology '$json_use.topology' --assembly_plan_name '$json_use.assembly_plan_name' @@ -52,7 +52,10 @@ - + + + + @@ -99,7 +102,7 @@ - + @@ -144,7 +147,7 @@ - + @@ -185,7 +188,7 @@ - + @@ -214,7 +217,7 @@ - + @@ -243,7 +246,7 @@ - + @@ -289,7 +292,7 @@ - + @@ -354,7 +357,7 @@ - + @@ -410,7 +413,7 @@ - + @@ -450,12 +453,12 @@ `_). **Parameters**: ---------------- +---------------- * **Use parameters from JSON**: Yes/No parameter to ask user if he wants to set parameters manually or using JSON file. * **Assemby csv**: csv file containes the construct names with their parts. (Without Header) * **GenBank files**: Upload all the parts sequences for your assembli(es). Don't forget the receptor vector(s). @@ -463,11 +466,11 @@ * **Topology**: Can be "circular", "linear". * **Enzyme**: It will be selected automatically, or you can set one from this dictionnary : `dict `_ * **Assembly Class**: - - "GoldenGate_assembly": Type2sRestrictionAssembly (recommended in Domesticated dataset) `ex. dataset `_ - - "gibson_assembly": GibsonAssembly `ex. dataset `_ - - "BASIC_assembly": BASICAssembly `ex. dataset `_ - - "biobrick_assembly": BioBrickStandardAssembly, `ex. dataset `_ - - "lcr_assembly": LigaseCyclingReactionAssembly `ex. dataset `_ + - "GoldenGate_assembly": Type2sRestrictionAssembly (recommended in Domesticated dataset) `Golden Gate dataset `_ + - "gibson_assembly": GibsonAssembly `Gibson dataset `_ + - "BASIC_assembly": BASICAssembly `BASIC dataset `_ + - "biobrick_assembly": BioBrickStandardAssembly, `biobrick dataset `_ + - "lcr_assembly": LigaseCyclingReactionAssembly `lcr dataset `_ ]]> diff -r 2655e08cd61a -r e7ecf6e21b49 output.html --- a/output.html Wed Jul 23 09:46:59 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,291 +0,0 @@ - - - - - - - Test Results (powered by Planemo) - - - - - - - - - - -
-
-
-
- - - - - - - \ No newline at end of file diff -r 2655e08cd61a -r e7ecf6e21b49 output.json --- a/output.json Wed Jul 23 09:46:59 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1986 +0,0 @@ -{ - "summary": { - "num_errors": 0, - "num_failures": 0, - "num_skips": 0, - "num_tests": 7 - }, - "tests": [ - { - "data": { - "inputs": { - "adv|use_file_names_as_ids": true, - "assembly_csv": { - "id": "5251f3a41a1cbe5c", - "src": "hda" - }, - "assembly_plan_name": "Type2sRestrictionAssembly", - "genbank_files": { - "id": "b685bcc6830b171b", - "src": "hdca" - }, - "topology": "circular" - }, - "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp2jitj5ti/files/c/2/9/dataset_c29f7add-5948-4171-8ac2-f87d5bf0f6f6.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp2jitj5ti/files/e/6/3/dataset_e63928a2-379c-45c8-8839-98a0df69a5cb.dat,/tmp/tmp2jitj5ti/files/4/4/7/dataset_44790451-2c88-485c-b4d5-d0f4bf78a093.dat,/tmp/tmp2jitj5ti/files/7/3/5/dataset_7354b218-2236-4b40-bdcb-3a46917a6e0f.dat,/tmp/tmp2jitj5ti/files/a/8/e/dataset_a8e12f0e-8a7c-48dd-a8ef-6988c90a7e58.dat,/tmp/tmp2jitj5ti/files/a/2/9/dataset_a298e5dd-536e-4652-8690-5132027c738c.dat,/tmp/tmp2jitj5ti/files/d/c/d/dataset_dcd006e1-e03f-42ed-b029-00134dd29dd1.dat,/tmp/tmp2jitj5ti/files/2/a/f/dataset_2aff75ea-f829-4836-a3dc-7cb018e02383.dat,/tmp/tmp2jitj5ti/files/a/1/8/dataset_a180d7ab-0c41-48d4-8941-3d8d251808a6.dat,/tmp/tmp2jitj5ti/files/6/9/2/dataset_692e75b8-b311-48e4-9b81-92c7addf1f79.dat,/tmp/tmp2jitj5ti/files/9/b/3/dataset_9b37829a-f97b-4f67-8243-bf2bd14ae4b6.dat,/tmp/tmp2jitj5ti/files/c/1/2/dataset_c12c0090-a770-4e92-9398-1a66760dc274.dat,/tmp/tmp2jitj5ti/files/5/2/1/dataset_521c5340-7b41-4b46-aa04-9be9ab5e99fd.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmp2jitj5ti/files/e/6/3/dataset_e63928a2-379c-45c8-8839-98a0df69a5cb.dat:part_A.gb,/tmp/tmp2jitj5ti/files/4/4/7/dataset_44790451-2c88-485c-b4d5-d0f4bf78a093.dat:part_B.gb,/tmp/tmp2jitj5ti/files/7/3/5/dataset_7354b218-2236-4b40-bdcb-3a46917a6e0f.dat:part_C.gb,/tmp/tmp2jitj5ti/files/a/8/e/dataset_a8e12f0e-8a7c-48dd-a8ef-6988c90a7e58.dat:part_D.gb,/tmp/tmp2jitj5ti/files/a/2/9/dataset_a298e5dd-536e-4652-8690-5132027c738c.dat:part_E.gb,/tmp/tmp2jitj5ti/files/d/c/d/dataset_dcd006e1-e03f-42ed-b029-00134dd29dd1.dat:part_F.gb,/tmp/tmp2jitj5ti/files/2/a/f/dataset_2aff75ea-f829-4836-a3dc-7cb018e02383.dat:part_G.gb,/tmp/tmp2jitj5ti/files/a/1/8/dataset_a180d7ab-0c41-48d4-8941-3d8d251808a6.dat:part_H.gb,/tmp/tmp2jitj5ti/files/6/9/2/dataset_692e75b8-b311-48e4-9b81-92c7addf1f79.dat:part_I.gb,/tmp/tmp2jitj5ti/files/9/b/3/dataset_9b37829a-f97b-4f67-8243-bf2bd14ae4b6.dat:part_J.gb,/tmp/tmp2jitj5ti/files/c/1/2/dataset_c12c0090-a770-4e92-9398-1a66760dc274.dat:part_K.gb,/tmp/tmp2jitj5ti/files/5/2/1/dataset_521c5340-7b41-4b46-aa04-9be9ab5e99fd.dat:part_L.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp2jitj5ti/job_working_directory/000/14/outputs/dataset_d929e00d-64fe-466c-820f-898fef1ddd39.dat'", - "command_version": "", - "copied_from_job_id": null, - "create_time": "2025-06-06T10:05:03.918951", - "dependencies": [], - "exit_code": 0, - "external_id": "384868", - "galaxy_version": "24.2", - "handler": null, - "history_id": "b685bcc6830b171b", - "id": "382e0b9a3dd586fb", - "inputs": { - "assembly_csv": { - "id": "5251f3a41a1cbe5c", - "src": "hda", - "uuid": "c29f7add-5948-4171-8ac2-f87d5bf0f6f6" - }, - "genbank_files1": { - "id": "b685bcc6830b171b", - "src": "hda", - "uuid": "e63928a2-379c-45c8-8839-98a0df69a5cb" - }, - "genbank_files10": { - "id": "07723b52981231a1", - "src": "hda", - "uuid": "9b37829a-f97b-4f67-8243-bf2bd14ae4b6" - }, - "genbank_files11": { - "id": "830f955cbdf9a561", - "src": "hda", - "uuid": "c12c0090-a770-4e92-9398-1a66760dc274" - }, - "genbank_files12": { - "id": "71dab170b139725e", - "src": "hda", - "uuid": "521c5340-7b41-4b46-aa04-9be9ab5e99fd" - }, - "genbank_files2": { - "id": "48e269c64ce4fce2", - "src": "hda", - "uuid": "44790451-2c88-485c-b4d5-d0f4bf78a093" - }, - "genbank_files3": { - "id": "abbe1d9cd04428c7", - "src": "hda", - "uuid": "7354b218-2236-4b40-bdcb-3a46917a6e0f" - }, - "genbank_files4": { - "id": "b93fb7c1f8bf7b46", - "src": "hda", - "uuid": "a8e12f0e-8a7c-48dd-a8ef-6988c90a7e58" - }, - "genbank_files5": { - "id": "45bf0c3ad4473005", - "src": "hda", - "uuid": "a298e5dd-536e-4652-8690-5132027c738c" - }, - "genbank_files6": { - "id": "4efa4181abcbfe3f", - "src": "hda", - "uuid": "dcd006e1-e03f-42ed-b029-00134dd29dd1" - }, - "genbank_files7": { - "id": "beb5db8871971f36", - "src": "hda", - "uuid": "2aff75ea-f829-4836-a3dc-7cb018e02383" - }, - "genbank_files8": { - "id": "bc095eef87c18a70", - "src": "hda", - "uuid": "a180d7ab-0c41-48d4-8941-3d8d251808a6" - }, - "genbank_files9": { - "id": "9f6ba43f26fd6d3f", - "src": "hda", - "uuid": "692e75b8-b311-48e4-9b81-92c7addf1f79" - } - }, - "job_messages": [], - "job_metrics": [], - "job_runner_name": null, - "job_stderr": "", - "job_stdout": "", - "model_class": "Job", - "output_collections": { - "construct_gb": { - "id": "48e269c64ce4fce2", - "src": "hdca" - } - }, - "outputs": { - "__new_primary_file_construct_gb|construct_1__": { - "id": "56254918ce4e0956", - "src": "hda", - "uuid": "41a51dd8-721c-4361-8c96-d4e737f41eec" - }, - "__new_primary_file_construct_gb|construct_2__": { - "id": "aad815be3bbd2bd5", - "src": "hda", - "uuid": "956b70c1-92eb-422d-ab4f-808a8b962d1f" - }, - "__new_primary_file_construct_gb|construct_3__": { - "id": "720f24a804e8d612", - "src": "hda", - "uuid": "998417d6-f292-4477-a81c-962b56e7a0e0" - }, - "__new_primary_file_construct_gb|construct_4__": { - "id": "d6de5bc932d51475", - "src": "hda", - "uuid": "e7c25803-f52c-4a42-8dc6-c9191701d749" - }, - "output_zip": { - "id": "382e0b9a3dd586fb", - "src": "hda", - "uuid": "d929e00d-64fe-466c-820f-898fef1ddd39" - } - }, - "params": { - "__input_ext": "\"input\"", - "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", - "assembly_plan_name": "\"Type2sRestrictionAssembly\"", - "chromInfo": "\"/tmp/tmp2jitj5ti/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", - "dbkey": "\"?\"", - "domesticated_input": null, - "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}", - "topology": "\"circular\"" - }, - "state": "ok", - "stderr": "\rassembly: 0%| | 0/4 [00:00