diff --git a/workflows/computational-chemistry/gromacs-mmgbsa/CHANGELOG.md b/workflows/computational-chemistry/gromacs-mmgbsa/CHANGELOG.md index 27519c696..69007db6a 100644 --- a/workflows/computational-chemistry/gromacs-mmgbsa/CHANGELOG.md +++ b/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 diff --git a/workflows/computational-chemistry/gromacs-mmgbsa/gromacs-mmgbsa-tests.yml b/workflows/computational-chemistry/gromacs-mmgbsa/gromacs-mmgbsa-tests.yml index 9078bd0a5..aad5280a1 100644 --- a/workflows/computational-chemistry/gromacs-mmgbsa/gromacs-mmgbsa-tests.yml +++ b/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 diff --git a/workflows/computational-chemistry/gromacs-mmgbsa/gromacs-mmgbsa.ga b/workflows/computational-chemistry/gromacs-mmgbsa/gromacs-mmgbsa.ga index 3db8129e9..8d5169b78 100644 --- a/workflows/computational-chemistry/gromacs-mmgbsa/gromacs-mmgbsa.ga +++ b/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,