Mercurial > repos > tduigou > genetic_design_workflow
view Genetic_Design_Workflow.ga @ 0:0cf30759d085 draft
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author | tduigou |
---|---|
date | Tue, 21 Dec 2021 13:15:48 +0000 |
parents | |
children |
line wrap: on
line source
{ "a_galaxy_workflow": "true", "annotation": "", "format-version": "0.1", "name": "Genetic_Design_Workflow", "steps": { "0": { "annotation": "", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { "description": "", "name": "SBML Pathway" } ], "label": "SBML Pathway", "name": "Input dataset", "outputs": [], "position": { "bottom": 393.8000030517578, "height": 61.80000305175781, "left": -68, "right": 132, "top": 332, "width": 200, "x": -68, "y": 332 }, "tool_id": null, "tool_state": "{\"optional\": false}", "tool_version": null, "type": "data_input", "uuid": "e0c30803-3cb9-41f0-9474-f5f9d1d1e5ad", "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "c6ae200e-5f3c-43d0-a3c0-2a13a1649b32" } ] }, "1": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.1.0", "errors": null, "id": 1, "input_connections": { "pathway": { "id": 0, "output_name": "output" } }, "inputs": [], "label": null, "name": "Selenzyme", "outputs": [ { "name": "uniprot_ids", "type": "xml" }, { "name": "uniprot_ids_csv", "type": "csv" } ], "position": { "bottom": 611.6000061035156, "height": 123.60000610351562, "left": 152.25, "right": 352.25, "top": 488, "width": 200, "x": 152.25, "y": 488 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.1.0", "tool_shed_repository": { "changeset_revision": "481f7c35323d", "name": "selenzy", "owner": "tduigou", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"adv\": {\"nb_ids\": \"-1\", \"nb_targets\": \"500\", \"direction\": \"0.0\", \"NoMSA\": \"true\", \"taxonIDs\": \"83333\"}, \"pathway\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.1.0", "type": "tool", "uuid": "14aad2ec-173e-4d6b-9a4e-6a377c01eb47", "workflow_outputs": [ { "label": "Uniprot IDs", "output_name": "uniprot_ids", "uuid": "dd39886f-4a0a-4b19-ab49-ce78fd6c3e78" }, { "label": "Uniprot IDs", "output_name": "uniprot_ids_csv", "uuid": "eb5292b9-77e2-48f6-9f7a-c9f99c94c5f0" } ] }, "2": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/sbml2sbol/sbml2sbol/0.1.12", "errors": null, "id": 2, "input_connections": { "sbml_single_input": { "id": 1, "output_name": "uniprot_ids" } }, "inputs": [], "label": null, "name": "SbmlToSbol", "outputs": [ { "name": "sbol_outfile", "type": "xml" } ], "position": { "bottom": 536.6000061035156, "height": 113.60000610351562, "left": 433.5, "right": 633.5, "top": 423, "width": 200, "x": 433.5, "y": 423 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/sbml2sbol/sbml2sbol/0.1.12", "tool_shed_repository": { "changeset_revision": "f0a06f526c7f", "name": "sbml2sbol", "owner": "tduigou", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"adv\": {\"rbs\": \"true\", \"max_prot_per_react\": \"3\", \"tirs\": \"\", \"pathway_id\": \"rp_pathway\", \"uniprotID_key\": \"selenzy\"}, \"sbml_single_input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.1.12", "type": "tool", "uuid": "585d5a08-f0c2-4a87-b3ca-ce9e809ad7bb", "workflow_outputs": [ { "label": "SbmlToSbol: sbol outfile", "output_name": "sbol_outfile", "uuid": "0ab3c9d1-82fb-4295-89ad-02e8c5dc0e64" } ] }, "3": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/partsgenie/PartsGenie/1.0.1", "errors": null, "id": 3, "input_connections": { "enzymes_file": { "id": 2, "output_name": "sbol_outfile" } }, "inputs": [ { "description": "runtime parameter for tool PartsGenie", "name": "enzymes_file" } ], "label": null, "name": "PartsGenie", "outputs": [ { "name": "parts", "type": "xml" } ], "position": { "bottom": 484.1999969482422, "height": 93.19999694824219, "left": 692, "right": 892, "top": 391, "width": 200, "x": 692, "y": 391 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/partsgenie/PartsGenie/1.0.1", "tool_shed_repository": { "changeset_revision": "295a21fc55d0", "name": "partsgenie", "owner": "tduigou", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"adv\": {\"url\": \"https://partsgenie.micalis.inrae.fr\"}, \"enzymes_file\": {\"__class__\": \"RuntimeValue\"}, \"taxonomy_id\": \"83333\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.1", "type": "tool", "uuid": "a6dd01a2-6def-4872-89d0-c762b7e6e1ca", "workflow_outputs": [ { "label": "Parts", "output_name": "parts", "uuid": "73bc4334-9596-47f8-9fc3-a6e4767e97bb" } ] }, "4": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/optdoe/OptDoE/2.0.1", "errors": null, "id": 4, "input_connections": { "adv|genes_sbol_file": { "id": 3, "output_name": "parts" }, "genes_file": { "id": 1, "output_name": "uniprot_ids_csv" } }, "inputs": [ { "description": "runtime parameter for tool Design of Experiment", "name": "adv" } ], "label": null, "name": "Design of Experiment", "outputs": [ { "name": "constructs", "type": "xml" } ], "position": { "bottom": 693.8999938964844, "height": 174.39999389648438, "left": 939.5, "right": 1139.5, "top": 519.5, "width": 200, "x": 939.5, "y": 519.5 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/optdoe/OptDoE/2.0.1", "tool_shed_repository": { "changeset_revision": "7f13e58f1532", "name": "optdoe", "owner": "tduigou", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"adv\": {\"genes_sbol_file\": {\"__class__\": \"ConnectedValue\"}, \"ref_parts_file\": {\"__class__\": \"RuntimeValue\"}, \"libsize\": \"32\", \"get_sequences\": \"true\", \"backtranslate\": \"true\", \"codon_table\": \"Eecoli.cut\"}, \"genes_file\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.0.1", "type": "tool", "uuid": "b9872d59-e433-4e31-8dc2-c00fd03c7a83", "workflow_outputs": [ { "label": "Constructs", "output_name": "constructs", "uuid": "d677903a-dd9b-4deb-a09a-7c81b7803dac" } ] }, "5": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/dnaweaver/DNAWeaver/1.0.1", "errors": null, "id": 5, "input_connections": { "input": { "id": 4, "output_name": "constructs" } }, "inputs": [], "label": null, "name": "DNA Weaver", "outputs": [ { "name": "output", "type": "xlsx" } ], "position": { "bottom": 631.9499969482422, "height": 93.19999694824219, "left": 1222.25, "right": 1422.25, "top": 538.75, "width": 200, "x": 1222.25, "y": 538.75 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/dnaweaver/DNAWeaver/1.0.1", "tool_shed_repository": { "changeset_revision": "90025c4cd50e", "name": "dnaweaver", "owner": "tduigou", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"adv\": {\"max_constructs\": \"-1\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"method\": \"golden_gate\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.1", "type": "tool", "uuid": "c045b22d-b1df-4620-80fe-d22c335b7e78", "workflow_outputs": [ { "label": "Assembly Plan", "output_name": "output", "uuid": "42769098-1a73-4c65-ac2d-e0a54d9f2ea2" } ] }, "6": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/lcrgenie/LCRGenie/1.0.1", "errors": null, "id": 6, "input_connections": { "LCR_input": { "id": 4, "output_name": "constructs" } }, "inputs": [], "label": null, "name": "LCR Genie", "outputs": [ { "name": "LCR_output", "type": "xlsx" } ], "position": { "bottom": 802.6000061035156, "height": 113.60000610351562, "left": 1224.5, "right": 1424.5, "top": 689, "width": 200, "x": 1224.5, "y": 689 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/lcrgenie/LCRGenie/1.0.1", "tool_shed_repository": { "changeset_revision": "71568c0c83f4", "name": "lcrgenie", "owner": "tduigou", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"LCR_input\": {\"__class__\": \"ConnectedValue\"}, \"adv\": {\"melting_temp\": \"60.0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.1", "type": "tool", "uuid": "14974d0a-257e-4cba-8bea-37367638750e", "workflow_outputs": [ { "label": "LCR Genie: Assembly Plan", "output_name": "LCR_output", "uuid": "ba05b6d0-a81f-496f-925b-bc2a9e014eac" } ] } }, "tags": [], "uuid": "156b3f3d-9925-48fc-bb22-cfff50584c3e", "version": 6 }