config_tag_pdb2gmx plugin

utils/config-tag-pdb2gmx-plugin/.bumpversion.cfg

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+[bumpversion]
+current_version = 0.1.0
+commit = False
+tag = False
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
+serialize = 
+	{major}.{minor}.{patch}-{release}{dev}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+optional_value = _
+first_value = dev
+values = 
+	dev
+	_
+
+[bumpversion:part:dev]
+
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
+[bumpversion:file:VERSION]
+
+[bumpversion:file:README.md]
+
+[bumpversion:file:plugin.json]
+
+[bumpversion:file:src/polus/mm/utils/config_tag_pdb2gmx/__init__.py]

utils/config-tag-pdb2gmx-plugin/.dockerignore

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+.venv
+out
+tests
+__pycache__

utils/config-tag-pdb2gmx-plugin/.gitignore

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+poetry.lock

utils/config-tag-pdb2gmx-plugin/CHANGELOG.md

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+# CHANGELOG
+
+## 0.1.0
+
+Initial release.

utils/config-tag-pdb2gmx-plugin/README.md

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+# config_tag_pdb2gmx (0.1.0)
+
+Returns a dictionary of the given arguments as a JSON-encoded string.
+
+## Options
+
+This plugin takes 4 input arguments and 1 output argument:
+
+| Name          | Description             | I/O    | Type   | Default |
+|---------------|-------------------------|--------|--------|---------|
+| water_type |  | Input | string | string |
+| forcefield |  | Input | string | string |
+| ignh |  | Input | boolean | boolean |
+| merge |  | Input | boolean | boolean |
+| output_config_string | A dictionary of the given arguments as a JSON-encoded string. | Output | string | string |

utils/config-tag-pdb2gmx-plugin/VERSION

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+0.1.0

utils/config-tag-pdb2gmx-plugin/config_tag_pdb2gmx.cwl

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+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.0
+
+label: Returns a dictionary of the given arguments as a JSON-encoded string.
+doc: |-
+  Returns a dictionary of the given arguments as a JSON-encoded string.
+
+baseCommand: echo # Anything, unused
+
+requirements:
+  InlineJavascriptRequirement: {}
+
+inputs:
+  water_type:
+    type: string
+    format:
+    - edam:format_2330
+
+  forcefield:
+    type: string
+    format: edam:format_2330
+
+  ignh:
+    type: boolean
+    format: edam:format_2330
+
+  merge:
+    type: boolean
+    format: edam:format_2330
+
+# TODO: his
+
+outputs:
+  output_config_string:
+    label: A dictionary of the given arguments as a JSON-encoded string.
+    doc: |-
+      A dictionary of the given arguments as a JSON-encoded string.
+    type: string
+    #format: edam:format_2330 # "'str' object does not support item assignment""
+    outputBinding:
+      outputEval: |
+        ${
+          var config = {};
+          config["water_type"] = inputs.water_type;
+          config["force_field"] = inputs.forcefield; // Note underscore
+          config["ignh"] = inputs.ignh;
+          config["merge"] = inputs.merge;
+          return JSON.stringify(config);
+        }
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

utils/config-tag-pdb2gmx-plugin/ict.yml

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+specVersion: "0.1.0"
+name: config_tag_pdb2gmx
+version: 0.1.0
+container: config-tag-pdb2gmx-plugin
+entrypoint:
+title: config_tag_pdb2gmx
+description: Returns a dictionary of the given arguments as a JSON-encoded string.
+author: Data Scientist
+contact: [email protected]
+repository:
+documentation:
+citation:
+
+inputs:
+  - name: water_type
+    required: true
+    description:
+    type: string
+    format:
+      uri: edam:format_2330
+  - name: forcefield
+    required: true
+    description:
+    type: string
+    format:
+      uri: edam:format_2330
+  - name: ignh
+    required: true
+    description:
+    type: boolean
+    format:
+      uri: edam:format_2330
+  - name: merge
+    required: true
+    description:
+    type: boolean
+    format:
+      uri: edam:format_2330
+outputs:
+  - name: output_config_string
+    required: true
+    description: A dictionary of the given arguments as a JSON-encoded string.
+    type: string
+ui:
+  - key: inputs.water_type
+    title: "water_type: "
+    description: ""
+    type: string
+  - key: inputs.forcefield
+    title: "forcefield: "
+    description: ""
+    type: string
+  - key: inputs.ignh
+    title: "ignh: "
+    description: ""
+    type: checkbox
+  - key: inputs.merge
+    title: "merge: "
+    description: ""
+    type: checkbox

utils/config-tag-pdb2gmx-plugin/pyproject.toml

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+[tool.poetry]
+name = "polus-mm-utils-config-tag-pdb2gmx"
+version = "0.1.0"
+description = "Returns a dictionary of the given arguments as a JSON-encoded string."
+authors = ["Data Scientist <[email protected]>"]
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = ">=3.9,<3.12"
+typer = "^0.7.0"
+cwl-utils = "0.33"
+cwltool = "3.1.20240404144621"
+
+[tool.poetry.group.dev.dependencies]
+bump2version = "^1.0.1"
+pytest = "^7.4"
+pytest-sugar = "^0.9.6"
+pre-commit = "^3.2.1"
+black = "^23.3.0"
+mypy = "^1.1.1"
+ruff = "^0.0.270"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.pytest.ini_options]
+pythonpath = [
+  "."
+]

utils/config-tag-pdb2gmx-plugin/tests/__init__.py

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+"""Tests for config_tag_pdb2gmx."""

utils/config-tag-pdb2gmx-plugin/tests/test_config_tag_pdb2gmx.py

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+"""Tests for config_tag_pdb2gmx."""
+import sys
+from pathlib import Path
+
+current_dir = Path(__file__).resolve().parent
+target_dir = current_dir.parent.parent.parent / "cwl_utils"
+sys.path.append(str(target_dir))
+
+from cwl_utilities import call_cwltool  # noqa: E402
+from cwl_utilities import create_input_yaml  # noqa: E402
+from cwl_utilities import parse_cwl_arguments  # noqa: E402
+
+
+def test_config_tag_pdb2gmx() -> None:
+    """Test config_tag_pdb2gmx."""
+    cwl_file = Path("config_tag_pdb2gmx.cwl")
+    input_to_props = parse_cwl_arguments(cwl_file)
+
+    input_to_props["water_type"] = "spec"
+    input_to_props["forcefield"] = "mber99sb-ildn"
+    input_to_props["ignh"] = True
+    input_to_props["merge"] = False
+    input_yaml_path = Path("config_tag_pdb2gmx.yml")
+
+    create_input_yaml(input_to_props, input_yaml_path)
+    stdout, stderr = call_cwltool(cwl_file, input_yaml_path)
+    assert "success" in stderr