extract-model (#62)

Co-authored-by: Brandon Duane Walker <[email protected]>

utils/extract-model-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/extract_model/__init__.py]

utils/extract-model-plugin/.dockerignore

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+.venv
+out
+tests
+__pycache__

utils/extract-model-plugin/.gitignore

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+poetry.lock

utils/extract-model-plugin/CHANGELOG.md

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

utils/extract-model-plugin/README.md

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+# extract_model (0.1.0)
+
+This class is a wrapper of the Structure Checking tool to extract a model from a 3D structure.
+
+## Options
+
+This plugin takes 3 input arguments and 1 output argument:
+
+| Name          | Description             | I/O    | Type   | Default |
+|---------------|-------------------------|--------|--------|---------|
+| input_structure_path | Input structure file path, Type: string, File type: input, Accepted formats: pdb, pdbqt, Example file: https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/extract_model.pdb | Input | File | File |
+| output_structure_path | Output structure file path, Type: string, File type: output, Accepted formats: pdb, pdbqt, Example file: https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_extract_model.pdb | Input | string | string |
+| config | Advanced configuration options for biobb_structure_utils ExtractModel. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_structure_utils ExtractModel documentation: https://biobb-structure-utils.readthedocs.io/en/latest/utils.html#module-utils.extract_model | Input | string | string |
+| output_structure_path | Output structure file path | Output | File | File |

utils/extract-model-plugin/VERSION

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+0.1.0

utils/extract-model-plugin/extract_model.cwl

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+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+label: This class is a wrapper of the Structure Checking tool to extract a model from
+  a 3D structure.
+
+doc: |-
+  Wrapper for the Structure Checking tool to extract a model from a 3D structure.
+
+baseCommand: extract_model
+
+hints:
+  DockerRequirement:
+    dockerPull: quay.io/biocontainers/biobb_structure_utils:4.0.0--pyhdfd78af_0  # 4.0.0--pyhdfd78af_1 Doesn't work!
+
+
+inputs:
+  input_structure_path:
+    label: Input structure file path
+    doc: |-
+      Input structure file path
+      Type: string
+      File type: input
+      Accepted formats: pdb, pdbqt
+      Example file: https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/extract_model.pdb
+    type: File
+    format: edam:format_1476, edam:format_1476
+    inputBinding:
+      position: 1
+      prefix: --input_structure_path
+
+  output_structure_path:
+    label: Output structure file path
+    doc: |-
+      Output structure file path
+      Type: string
+      File type: output
+      Accepted formats: pdb, pdbqt
+      Example file: https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_extract_model.pdb
+    type: string
+    format: edam:format_1476, edam:format_1476
+    inputBinding:
+      position: 2
+      prefix: --output_structure_path
+    default: system.pdb
+
+  config:
+    label: Advanced configuration options for biobb_structure_utils ExtractModel
+    doc: |-
+      Advanced configuration options for biobb_structure_utils ExtractModel. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_structure_utils ExtractModel documentation: https://biobb-structure-utils.readthedocs.io/en/latest/utils.html#module-utils.extract_model
+    type: string?
+    inputBinding:
+      prefix: --config
+
+outputs:
+  output_structure_path:
+    label: Output structure file path
+    doc: |-
+      Output structure file path
+    type: File
+    outputBinding:
+      glob: $(inputs.output_structure_path)
+    format: edam:format_1476
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

utils/extract-model-plugin/ict.yml

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+specVersion: "0.1.0"
+name: extract_model
+version: 0.1.0
+container: extract-model-plugin
+entrypoint:
+title: extract_model
+description: This class is a wrapper of the Structure Checking tool to extract a model from a 3D structure.
+author: Data Scientist
+contact: [email protected]
+repository:
+documentation:
+citation:
+
+inputs:
+  - name: input_structure_path
+    required: true
+    description: Input structure file path, Type string, File type input, Accepted formats pdb, pdbqt, Example file https//github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/extract_model.pdb
+    type: File
+    format:
+      uri: edam:format_1476, edam:format_1476
+  - name: output_structure_path
+    required: true
+    description: Output structure file path, Type string, File type output, Accepted formats pdb, pdbqt, Example file https//github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_extract_model.pdb
+    type: string
+    defaultValue: system.pdb
+    format:
+      uri: edam:format_1476, edam:format_1476
+  - name: config
+    required: true
+    description: Advanced configuration options for biobb_structure_utils ExtractModel. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_structure_utils ExtractModel documentation https//biobb-structure-utils.readthedocs.io/en/latest/utils.html#module-utils.extract_model
+    type: string
+outputs:
+  - name: output_structure_path
+    required: true
+    description: Output structure file path
+    type: File
+    format:
+      uri: edam:format_1476
+ui:
+  - key: inputs.input_structure_path
+    title: "input_structure_path: "
+    description: "Input structure file path, Type string, File type input, Accepted formats pdb, pdbqt, Example file https//github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/extract_model.pdb"
+    type: File
+  - key: inputs.output_structure_path
+    title: "output_structure_path: "
+    description: "Output structure file path, Type string, File type output, Accepted formats pdb, pdbqt, Example file https//github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_extract_model.pdb"
+    type: string
+  - key: inputs.config
+    title: "config: "
+    description: "Advanced configuration options for biobb_structure_utils ExtractModel. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_structure_utils ExtractModel documentation https//biobb-structure-utils.readthedocs.io/en/latest/utils.html#module-utils.extract_model"
+    type: string

utils/extract-model-plugin/pyproject.toml

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+[tool.poetry]
+name = "polus-mm-utils-extract-model"
+version = "0.1.0"
+description = "This class is a wrapper of the Structure Checking tool to extract a model from a 3D structure."
+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/extract-model-plugin/tests/__init__.py

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+"""Tests for extract_model."""