Mercurial > repos > tduigou > retrosynthesis_workflow

changeset 1:e5803ef59eb6 draft default tip

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Thu, 10 Feb 2022 11:07:28 +0000
parents 5aa8c015b750
children
files repository_dependencies.xml retrosynthesis_workflow.ga
diffstat 2 files changed, 88 insertions(+), 97 deletions(-) [+]
line wrap: on
line diff
--- 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 @@
 <?xml version="1.0" ?>
 <repositories description="retrosynthesis workflow">
-    <repository changeset_revision="024dcd6421db" name="rrparser" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu"/>
-    <repository changeset_revision="f664f3c3aca8" name="rpextractsink" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu"/>
-    <repository changeset_revision="6cdbb534cbca" name="retropath2" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu"/>
-    <repository changeset_revision="2782bee7c5a6" name="rp2paths" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu"/>
-    <repository changeset_revision="98d925a75257" name="rpcompletion" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu"/>
+    <repository name="rrparser" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="ea590c609fec"/>
+    <repository name="rpextractsink" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="47bb93e7832b"/>
+    <repository name="retropath2" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="9c8ac9980bd6"/>
+    <repository name="rp2paths" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="2782bee7c5a6"/>
+    <repository name="rpcompletion" owner="tduigou" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="b8242cf18cc0"/>
 </repositories>
--- 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": {
-                "bottom": 570.6999969482422,
+                "bottom": 655.1999969482422,
                 "height": 93.19999694824219,
-                "left": 516.5,
-                "right": 716.5,
-                "top": 477.5,
+                "left": 603.5,
+                "right": 803.5,
+                "top": 562,
                 "width": 200,
-                "x": 516.5,
-                "y": 477.5
+                "x": 603.5,
+                "y": 562
             },
             "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpextractsink/rpExtractSink/5.9.2",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpextractsink/rpextractsink/5.12.1",
             "tool_shed_repository": {
-                "changeset_revision": "f664f3c3aca8",
+                "changeset_revision": "47bb93e7832b",
                 "name": "rpextractsink",
                 "owner": "tduigou",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"adv\": {\"compartment_id\": \"MNXC3\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"remove_dead_end\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": null,
+            "tool_state": "{\"adv\": {\"remove_dead_end\": \"true\"}, \"compartment_id\": \"c\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "5.12.1",
             "type": "tool",
-            "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,
-                "left": 794.5,
-                "right": 994.5,
-                "top": 350.5,
+                "left": 900.5,
+                "right": 1100.5,
+                "top": 415,
                 "width": 200,
-                "x": 794.5,
-                "y": 350.5
+                "x": 900.5,
+                "y": 415
             },
             "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/2.0.4",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/2.3.0",
             "tool_shed_repository": {
-                "changeset_revision": "6cdbb534cbca",
+                "changeset_revision": "9c8ac9980bd6",
                 "name": "retropath2",
                 "owner": "tduigou",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"adv\": {\"max_steps\": \"3\", \"topx\": \"100\", \"dmin\": \"0\", \"dmax\": \"1000\", \"mwmax_source\": \"1000\", \"mwmax_cof\": \"1000\", \"timeout\": \"60\"}, \"rulesfile\": {\"__class__\": \"RuntimeValue\"}, \"sinkfile\": {\"__class__\": \"RuntimeValue\"}, \"source_inchi\": {\"__class__\": \"ConnectedValue\"}, \"source_name\": \"target\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": null,
+            "tool_state": "{\"adv\": {\"version\": \"r20220104\", \"topx\": \"100\", \"dmin\": \"0\", \"dmax\": \"1000\", \"mwmax_source\": \"1000\", \"timeout\": \"60\"}, \"max_steps\": \"3\", \"rulesfile\": {\"__class__\": \"ConnectedValue\"}, \"sinkfile\": {\"__class__\": \"ConnectedValue\"}, \"source_inchi_type\": {\"inchi_type\": \"string\", \"__current_case__\": 0, \"source_inchi\": {\"__class__\": \"ConnectedValue\"}}, \"source_name\": \"target\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "2.3.0",
             "type": "tool",
-            "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": {
-                "changeset_revision": "98d925a75257",
+                "changeset_revision": "b8242cf18cc0",
                 "name": "rpcompletion",
                 "owner": "tduigou",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"adv\": {\"max_subpaths_filter\": \"10\", \"upper_flux_bound\": \"999999\", \"lower_flux_bound\": \"0\"}, \"rp2_pathways\": {\"__class__\": \"ConnectedValue\"}, \"rp2paths_compounds\": {\"__class__\": \"ConnectedValue\"}, \"rp2paths_pathways\": {\"__class__\": \"ConnectedValue\"}, \"sink\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": null,
+            "tool_version": "5.12.1",
             "type": "tool",
-            "uuid": "bfc32617-1870-4240-8cf6-ea93da840007",
+            "uuid": "9acba2e0-e30c-47a7-8166-a6d694e425f8",
             "workflow_outputs": [
                 {
                     "label": "Complete Reactions",
                     "output_name": "pathways",
-                    "uuid": "b77df22c-2b09-4787-8762-18f3fd748aea"
+                    "uuid": "fd9a697a-6bf9-4b84-88bf-a1c749475e30"
                 }
             ]
         }
     },
     "tags": [],
-    "uuid": "a8283850-4dcb-4bd9-a11e-507bf58e8b4b",
-    "version": 8
+    "uuid": "c563c2dc-6f52-45c3-978a-43777561081d",
+    "version": 9
 }
\ No newline at end of file