Updating workflows/computational-chemistry/gromacs-mmgbsa from 0.1.5 to 0.1.6

workflows/computational-chemistry/gromacs-mmgbsa/CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.1.6] 2023-11-27
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/chemteam/md_converter/md_converter/1.9.6+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/chemteam/md_converter/md_converter/1.9.7+galaxy0`
+
 ## [0.1.5] 2023-11-27
 
 ### Automatic update

workflows/computational-chemistry/gromacs-mmgbsa/gromacs-mmgbsa-tests.yml

@@ -15,18 +15,21 @@
     Salt concentration: 0.1
   outputs:
     MMGBSA free energy:
-      class: 'File'
-      assert:
-        has_n_lines: 2
+      asserts:
+        has_n_lines:
+          n: 2
     MMGBSA statistics:
       element_tests:
         split_file_000000.txt:
-          assert:
-            has_text: 'DELTA TOTAL'
-            has_text: 'Generalized Born ESURF calculated using LCPO'
+          asserts:
+          - that: has_text
+            text: 'DELTA TOTAL'
+          - that: has_text
+            text: 'Generalized Born ESURF calculated using LCPO'
     XTC files:
       element_tests:
         split_file_000000.txt:
-          assert:
-            has_size: 138900
-            delta: 500
+          asserts:
+            has_size:
+              size: 138900
+              delta: 500

workflows/computational-chemistry/gromacs-mmgbsa/gromacs-mmgbsa.ga

@@ -11,7 +11,7 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "MMGBSA calculations with GROMACS",
-    "release": "0.1.5",
+    "release": "0.1.12",
     "steps": {
         "0": {
             "annotation": "NaCl concentration",
@@ -369,6 +369,7 @@
             "subworkflow": {
                 "a_galaxy_workflow": "true",
                 "annotation": "",
+                "comments": [],
                 "creator": [
                     {
                         "class": "Person",
@@ -731,7 +732,7 @@
                     },
                     "9": {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1",
                         "errors": null,
                         "id": 9,
                         "input_connections": {
@@ -760,15 +761,15 @@
                                 "output_name": "output"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "d698c222f354",
+                            "changeset_revision": "fbf99087e067",
                             "name": "text_processing",
                             "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
                         "tool_state": "{\"case_sensitive\": \"-i\", \"color\": \"NOCOLOR\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"\", \"lines_after\": \"0\", \"lines_before\": \"0\", \"regex_type\": \"-P\", \"url_paste\": \"HETATM\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
+                        "tool_version": "9.3+galaxy1",
                         "type": "tool",
                         "uuid": "be1e9539-c3ba-4c3c-a06f-a82c5b4d8437",
                         "when": null,
@@ -828,7 +829,12 @@
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool AnteChamber",
+                                "name": "allparams"
+                            }
+                        ],
                         "label": null,
                         "name": "AnteChamber",
                         "outputs": [
@@ -987,8 +993,8 @@
                         ]
                     }
                 },
-                "tags": "",
-                "uuid": "1a4e83d6-e4b2-4f01-bcd1-de564a96bf7e"
+                "tags": [],
+                "uuid": "59bf6031-e018-4a7b-9765-ec0aa56581f5"
             },
             "tool_id": null,
             "type": "subworkflow",
@@ -1014,7 +1020,7 @@
         },
         "12": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1",
             "errors": null,
             "id": 12,
             "input_connections": {
@@ -1047,15 +1053,15 @@
                     "output_name": "outfile"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1",
             "tool_shed_repository": {
-                "changeset_revision": "d698c222f354",
+                "changeset_revision": "fbf99087e067",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"token_set\": [{\"__index__\": 0, \"line\": {\"__class__\": \"ConnectedValue\"}, \"repeat_select\": {\"repeat_select_opts\": \"user\", \"__current_case__\": 0, \"times\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "1.1.0",
+            "tool_version": "9.3+galaxy1",
             "type": "tool",
             "uuid": "712bd247-7a81-4e77-ab1c-ba0e3f012d20",
             "when": null,
@@ -1108,7 +1114,7 @@
         },
         "14": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.1",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2",
             "errors": null,
             "id": 14,
             "input_connections": {
@@ -1117,7 +1123,12 @@
                     "output_name": "outfile"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Split file",
+                    "name": "split_parms"
+                }
+            ],
             "label": null,
             "name": "Split file",
             "outputs": [
@@ -1137,15 +1148,15 @@
                     "output_name": "list_output_txt"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.1",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2",
             "tool_shed_repository": {
-                "changeset_revision": "baabc30154cd",
+                "changeset_revision": "2dae863c8f42",
                 "name": "split_file_to_collection",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"split_parms\": {\"select_ftype\": \"txt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}, \"select_mode\": {\"mode\": \"chunk\", \"__current_case__\": 0, \"chunksize\": \"1\"}, \"newfilenames\": \"split_file\", \"select_allocate\": {\"allocate\": \"byrow\", \"__current_case__\": 2}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "0.5.1",
+            "tool_version": "0.5.2",
             "type": "tool",
             "uuid": "06f666f0-c2a8-4f18-9ad6-42b0e601c731",
             "when": null,
@@ -1334,7 +1345,16 @@
                     "output_name": "output2"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Convert Parameters",
+                    "name": "param_inputs"
+                },
+                {
+                    "description": "runtime parameter for tool Convert Parameters",
+                    "name": "param_inputs"
+                }
+            ],
             "label": null,
             "name": "Convert Parameters",
             "outputs": [
@@ -1423,6 +1443,10 @@
                     "description": "runtime parameter for tool GROMACS simulation",
                     "name": "inps"
                 },
+                {
+                    "description": "runtime parameter for tool GROMACS simulation",
+                    "name": "inps"
+                },
                 {
                     "description": "runtime parameter for tool GROMACS simulation",
                     "name": "inps"
@@ -1516,6 +1540,14 @@
                 }
             },
             "inputs": [
+                {
+                    "description": "runtime parameter for tool GROMACS simulation",
+                    "name": "inps"
+                },
+                {
+                    "description": "runtime parameter for tool GROMACS simulation",
+                    "name": "inps"
+                },
                 {
                     "description": "runtime parameter for tool GROMACS simulation",
                     "name": "inps"
@@ -1605,6 +1637,14 @@
                 }
             },
             "inputs": [
+                {
+                    "description": "runtime parameter for tool GROMACS simulation",
+                    "name": "inps"
+                },
+                {
+                    "description": "runtime parameter for tool GROMACS simulation",
+                    "name": "inps"
+                },
                 {
                     "description": "runtime parameter for tool GROMACS simulation",
                     "name": "inps"
@@ -1805,7 +1845,7 @@
         },
         "24": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1",
             "errors": null,
             "id": 24,
             "input_connections": {
@@ -1834,15 +1874,15 @@
                     "output_name": "output"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1",
             "tool_shed_repository": {
-                "changeset_revision": "d698c222f354",
+                "changeset_revision": "fbf99087e067",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"case_sensitive\": \"-i\", \"color\": \"NOCOLOR\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"\", \"lines_after\": \"0\", \"lines_before\": \"0\", \"regex_type\": \"-P\", \"url_paste\": \"DELTA TOTAL\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "1.1.1",
+            "tool_version": "9.3+galaxy1",
             "type": "tool",
             "uuid": "3aba0217-8162-43c3-8d19-1b04dcb3984d",
             "when": null,