convert_xyz plugin (#43)

utils/convert-xyz-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/convert_xyz/__init__.py]

utils/convert-xyz-plugin/.dockerignore

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+.venv
+out
+tests
+__pycache__

utils/convert-xyz-plugin/.gitignore

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+poetry.lock

utils/convert-xyz-plugin/CHANGELOG.md

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

utils/convert-xyz-plugin/README.md

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+# convert_xyz (0.1.0)
+
+This class is a wrapper of the Open Babel tool.
+
+## Options
+
+This plugin takes 2 input arguments and 1 output argument:
+
+| Name          | Description             | I/O    | Type   | Default |
+|---------------|-------------------------|--------|--------|---------|
+| input_path | Path to the input file, Type: string, File type: input, Accepted formats: gro, mol, mol2, pdb, pdbqt, sdf, Example file: https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/data/babel/babel.smi | Input | File | File |
+| output_xyz_path | Path to the output file, Type: string, File type: output, Accepted formats: xyz | Input | string | string |
+| output_xyz_path | Path to the output file | Output | File | File |

utils/convert-xyz-plugin/VERSION

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+0.1.0

utils/convert-xyz-plugin/convert_xyz.cwl

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+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+
+class: CommandLineTool
+
+label: This class is a wrapper of the Open Babel tool.
+
+doc: |-
+  Converts small molecules in 2D or 3D formats to the XYZ format.
+
+baseCommand: obabel
+#Usage:
+#obabel[-i<input-type>] <infilename> [-o<output-type>] -O<outfilename> [Options]
+#...
+#Options, other than -i -o -O -m, must come after the input files.
+arguments: [$(inputs.input_path), "-o", "xyz", "-O", $(inputs.output_xyz_path)]
+
+hints:
+  DockerRequirement:
+    dockerPull: quay.io/biocontainers/biobb_chemistry:4.0.0--pyhdfd78af_1
+
+requirements:
+  InlineJavascriptRequirement: {}
+
+inputs:
+  input_path:
+    label: Path to the input file
+    doc: |-
+      Path to the input file
+      Type: string
+      File type: input
+      Accepted formats: gro, mol, mol2, pdb, pdbqt, sdf
+      Example file: https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/data/babel/babel.smi
+    type: File
+    format: edam:format_2033, edam:format_3815, edam:format_3816, edam:format_1476, edam:format_1476, edam:format_3814
+
+  output_xyz_path:
+    label: Path to the output file
+    doc: |-
+      Path to the output file
+      Type: string
+      File type: output
+      Accepted formats: xyz
+    type: string
+    format: edam:format_3877 # xyz
+    default: system.xyz
+
+outputs:
+  output_xyz_path:
+    label: Path to the output file
+    doc: |-
+      Path to the output file
+    type: File
+    outputBinding:
+      glob: $(inputs.output_xyz_path)
+    format: edam:format_3877 # xyz
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

utils/convert-xyz-plugin/ict.yml

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+specVersion: "0.1.0"
+name: convert_xyz
+version: 0.1.0
+container: convert-xyz-plugin
+entrypoint:
+title: convert_xyz
+description: This class is a wrapper of the Open Babel tool.
+author: Data Scientist
+contact: [email protected]
+repository:
+documentation:
+citation:
+
+inputs:
+  - name: input_path
+    required: true
+    description: Path to the input file, Type string, File type input, Accepted formats gro, mol, mol2, pdb, pdbqt, sdf, Example file https//github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/data/babel/babel.smi
+    type: File
+    format:
+      uri: edam:format_2033, edam:format_3815, edam:format_3816, edam:format_1476, edam:format_1476, edam:format_3814
+  - name: output_xyz_path
+    required: true
+    description: Path to the output file, Type string, File type output, Accepted formats xyz
+    type: string
+    defaultValue: system.xyz
+    format:
+      uri: edam:format_3877
+outputs:
+  - name: output_xyz_path
+    required: true
+    description: Path to the output file
+    type: File
+    format:
+      uri: edam:format_3877
+ui:
+  - key: inputs.input_path
+    title: "input_path: "
+    description: "Path to the input file, Type string, File type input, Accepted formats gro, mol, mol2, pdb, pdbqt, sdf, Example file https//github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/data/babel/babel.smi"
+    type: File
+  - key: inputs.output_xyz_path
+    title: "output_xyz_path: "
+    description: "Path to the output file, Type string, File type output, Accepted formats xyz"
+    type: string

utils/convert-xyz-plugin/pyproject.toml

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+[tool.poetry]
+name = "polus-mm-utils-convert-xyz"
+version = "0.1.0"
+description = "This class is a wrapper of the Open Babel tool."
+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/convert-xyz-plugin/tests/__init__.py

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+"""Tests for convert_xyz."""