# HG changeset patch # User tduigou # Date 1644491248 0 # Node ID e5803ef59eb64a3634849d120da6cf57d183bb34 # Parent 5aa8c015b7505950f74ace1c7b4a697980f1196d "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty" diff -r 5aa8c015b750 -r e5803ef59eb6 repository_dependencies.xml --- a/repository_dependencies.xml Thu Dec 02 14:11:13 2021 +0000 +++ b/repository_dependencies.xml Thu Feb 10 11:07:28 2022 +0000 @@ -1,8 +1,8 @@ - - - - - + + + + + diff -r 5aa8c015b750 -r e5803ef59eb6 retrosynthesis_workflow.ga --- a/retrosynthesis_workflow.ga Thu Dec 02 14:11:13 2021 +0000 +++ b/retrosynthesis_workflow.ga Thu Feb 10 11:07:28 2022 +0000 @@ -2,7 +2,7 @@ "a_galaxy_workflow": "true", "annotation": "", "format-version": "0.1", - "name": "RetroSynthesis_workflow", + "name": "Copy of RetroSynthesis_workflow", "steps": { "0": { "annotation": "", @@ -20,14 +20,14 @@ "name": "Input dataset", "outputs": [], "position": { - "bottom": 335.3000030517578, + "bottom": 495.3000030517578, "height": 61.80000305175781, - "left": 278.5, - "right": 478.5, - "top": 273.5, + "left": 339, + "right": 539, + "top": 433.5, "width": 200, - "x": 278.5, - "y": 273.5 + "x": 339, + "y": 433.5 }, "tool_id": null, "tool_state": "{\"optional\": false}", @@ -38,13 +38,13 @@ { "label": null, "output_name": "output", - "uuid": "1fa2a565-bbb4-4817-a142-cb6614aeba85" + "uuid": "0d8c01b5-de3b-4f6c-816e-f3d50dc39f81" } ] }, "1": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.5", + "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.6", "errors": null, "id": 1, "input_connections": {}, @@ -58,32 +58,32 @@ } ], "position": { - "bottom": 281.1000061035156, + "bottom": 412.6000061035156, "height": 102.60000610351562, - "left": 530.5, - "right": 730.5, - "top": 178.5, + "left": 588.5, + "right": 788.5, + "top": 310, "width": 200, - "x": 530.5, - "y": 178.5 + "x": 588.5, + "y": 310 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.5", + "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.6", "tool_shed_repository": { - "changeset_revision": "024dcd6421db", + "changeset_revision": "ea590c609fec", "name": "rrparser", "owner": "tduigou", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"compress\": \"false\", \"diameters\": [\"2\", \"4\", \"6\", \"8\", \"10\", \"12\", \"14\", \"16\"], \"rules\": {\"type\": \"retro\", \"__current_case__\": 2}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_state": "{\"compress\": \"false\", \"diameters\": [\"2\", \"4\", \"6\", \"8\", \"10\", \"12\", \"14\", \"16\"], \"rules\": {\"type\": \"retro\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.4.6", "type": "tool", - "uuid": "e7a835df-5172-4fdf-a2a3-81c41a73bc00", + "uuid": "39cbe6d0-bd77-4b16-9154-39228a68c875", "workflow_outputs": [ { "label": "RRules Parser(retro, d=['2', '4', '6', '8', '10', '12', '14', '16'])", "output_name": "out_rules", - "uuid": "938b8abf-ce03-476e-b92a-39dd14cbd643" + "uuid": "2fb329ce-971d-4158-9ec7-9b82c1b39be2" } ] }, @@ -103,31 +103,31 @@ "name": "Input parameter", "outputs": [], "position": { - "bottom": 440.6999969482422, - "height": 82.19999694824219, - "left": 518, - "right": 718, - "top": 358.5, + "bottom": 544.1000061035156, + "height": 102.60000610351562, + "left": 601.5, + "right": 801.5, + "top": 441.5, "width": 200, - "x": 518, - "y": 358.5 + "x": 601.5, + "y": 441.5 }, "tool_id": null, - "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", + "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "95271805-5e3f-40d4-b262-f162cbb790eb", + "uuid": "9e4e8764-1433-4bd8-afc0-698fa591ce6d", "workflow_outputs": [ { "label": null, "output_name": "output", - "uuid": "ce569b93-19c3-4ea7-bbeb-824d8416bd80" + "uuid": "12fa5134-5f52-4ebf-9616-1692e7c2f016" } ] }, "3": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpextractsink/rpExtractSink/5.9.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpextractsink/rpextractsink/5.12.1", "errors": null, "id": 3, "input_connections": { @@ -146,38 +146,38 @@ } ], "position": { - 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"uuid": "b8c49635-e74d-41d6-b1ee-7881087039c9", + "uuid": "65ddba64-bea5-466a-ab26-ba1859009cde", "workflow_outputs": [ { "label": null, "output_name": "sink", - "uuid": "9398d924-57ce-4b29-924c-db2baec7f913" + "uuid": "c1f1add8-2a31-4849-9aea-312db78d9414" } ] }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/2.0.4", + "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/2.3.0", "errors": null, "id": 4, "input_connections": { @@ -189,21 +189,12 @@ "id": 3, "output_name": "sink" }, - "source_inchi": { + "source_inchi_type|source_inchi": { "id": 2, "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool RetroPath2.0", - "name": "rulesfile" - }, - { - "description": "runtime parameter for tool RetroPath2.0", - "name": "sinkfile" - } - ], + "inputs": [], "label": null, "name": "RetroPath2.0", "outputs": [ @@ -213,32 +204,32 @@ } ], "position": { - "bottom": 504.5, + "bottom": 569, "height": 154, - 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"uuid": "e705e614-950a-436a-96a8-f8e9bcc4bb64", + "uuid": "7dd663f6-6633-41f0-b9cd-4bf575f72b90", "workflow_outputs": [ { "label": "RetroPath2.0", "output_name": "Reaction_Network", - "uuid": "31cac3f6-2f12-48c4-b265-9d745d5ba36d" + "uuid": "48e8b7d2-f341-4cff-b410-30652e68dab4" } ] }, @@ -267,14 +258,14 @@ } ], "position": { - "bottom": 437.8999938964844, + "bottom": 526.3999938964844, "height": 164.39999389648438, - "left": 1050.5, - "right": 1250.5, - "top": 273.5, + "left": 1193.5, + "right": 1393.5, + "top": 362, "width": 200, - "x": 1050.5, - "y": 273.5 + "x": 1193.5, + "y": 362 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rp2paths/rp2paths/1.4.3", @@ -285,25 +276,25 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"adv\": {\"timeout\": \"1800\"}, \"rp2_pathways\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "1.4.3", "type": "tool", - "uuid": "3ebbcfa4-dd81-4200-b023-dbb445131657", + "uuid": "0d9f290f-a11c-4471-ba16-e0c561634be5", "workflow_outputs": [ { "label": "RP2paths (Pathways)", "output_name": "master_pathways", - "uuid": "9b5454c6-35e7-4632-96d3-2d75ba8b1afe" + "uuid": "2225e9b3-8984-4d53-9878-232b4f773869" }, { "label": "RP2paths (Compounds)", "output_name": "compounds", - "uuid": "fc35e5fb-8556-4c7f-b11f-45b93467f7f6" + "uuid": "651afa73-ad92-4296-b788-00bd78f6df32" } ] }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpcompletion/rpCompletion/5.9.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpcompletion/rpcompletion/5.12.1", "errors": null, "id": 6, "input_connections": { @@ -334,37 +325,37 @@ } ], "position": { - "bottom": 646.1000061035156, + "bottom": 807.6000061035156, "height": 245.60000610351562, - "left": 1323.5, - "right": 1523.5, - "top": 400.5, + "left": 1447.5, + "right": 1647.5, + "top": 562, "width": 200, - "x": 1323.5, - "y": 400.5 + "x": 1447.5, + "y": 562 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpcompletion/rpCompletion/5.9.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpcompletion/rpcompletion/5.12.1", "tool_shed_repository": { - 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