bash_xvg

utils/bash-xvg-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/bash_xvg/__init__.py]

utils/bash-xvg-plugin/.dockerignore

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+.venv
+out
+tests
+__pycache__

utils/bash-xvg-plugin/.gitignore

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+poetry.lock

utils/bash-xvg-plugin/CHANGELOG.md

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

utils/bash-xvg-plugin/Dockerfile

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+FROM bash
+
+ADD replace_first_column.sh .
+ADD Dockerfile .

utils/bash-xvg-plugin/README.md

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+# bash_xvg (0.1.0)
+
+Replace a column in one file with a column from another using AWK
+
+## Options
+
+This plugin takes 3 input arguments and 1 output argument:
+
+| Name          | Description             | I/O    | Type   | Default |
+|---------------|-------------------------|--------|--------|---------|
+| input_xvg1_path | Path to the first XVG file | Input | File | File |
+| input_xvg2_path | Path to the second XVG file | Input | File | File |
+| output_xvg_path | Path to the output XVG file | Input | string | string |
+| output_xvg_path | Path to the output XVG file | Output | File | File |

utils/bash-xvg-plugin/VERSION

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+0.1.0

utils/bash-xvg-plugin/bash_xvg.cwl

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+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+label: Replace a column in one file with a column from another using AWKK
+
+doc: |
+  Replace a column in one file with a column from another using AWK
+
+baseCommand: ["bash", "/replace_first_column.sh"]
+
+hints:
+  DockerRequirement:
+    dockerPull: ndonyapour/replace_first_column
+
+inputs:
+  input_xvg1_path:
+    label: Path to the first XVG file
+    doc: |-
+      Path to the first XVG file
+    type: File
+    format: edam:format_2030
+    inputBinding:
+      position: 1
+
+  input_xvg2_path:
+    label: Path to the second XVG file
+    doc: |-
+      Path to the second XVG file
+    type: File
+    format: edam:format_2030
+    inputBinding:
+      position: 2
+
+  output_xvg_path:
+    label: Path to the output XVG file
+    doc: |-
+      Path to the output XVG file
+    type: string
+    format: edam:format_2030
+    default: system.xvg
+
+outputs:
+  output_xvg_path:
+    label: Path to the output XVG file
+    doc: |-
+      Path to the output XVG file
+    type: File
+    format: edam:format_2030
+    streamable: true
+    outputBinding:
+      glob: $(inputs.output_xvg_path)
+
+stdout: $(inputs.output_xvg_path)
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

utils/bash-xvg-plugin/ict.yml

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+specVersion: "0.1.0"
+name: bash_xvg
+version: 0.1.0
+container: bash-xvg-plugin
+entrypoint:
+title: bash_xvg
+description: Replace a column in one file with a column from another using AWK
+author: Data Scientist
+contact: [email protected]
+repository:
+documentation:
+citation:
+
+inputs:
+  - name: input_xvg1_path
+    required: true
+    description: Path to the first XVG file
+    type: File
+    format:
+      uri: edam:format_2030
+  - name: input_xvg2_path
+    required: true
+    description: Path to the second XVG file
+    type: File
+    format:
+      uri: edam:format_2030
+  - name: output_xvg_path
+    required: true
+    description: Path to the output XVG file
+    type: string
+    defaultValue: system.xvg
+    format:
+      uri: edam:format_2030
+outputs:
+  - name: output_xvg_path
+    required: true
+    description: Path to the output XVG file
+    type: File
+    format:
+      uri: edam:format_2030
+ui:
+  - key: inputs.input_xvg1_path
+    title: "input_xvg1_path: "
+    description: "Path to the first XVG file"
+    type: File
+  - key: inputs.input_xvg2_path
+    title: "input_xvg2_path: "
+    description: "Path to the second XVG file"
+    type: File
+  - key: inputs.output_xvg_path
+    title: "output_xvg_path: "
+    description: "Path to the output XVG file"
+    type: string

utils/bash-xvg-plugin/pyproject.toml

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+[tool.poetry]
+name = "polus-mm-utils-bash-xvg"
+version = "0.1.0"
+description = "Replace a column in one file with a column from another using AWK"
+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/bash-xvg-plugin/replace_first_column.sh

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+#!/bin/bash -e
+# See https://stackoverflow.com/questions/7846476/replace-column-in-one-file-with-column-from-another-using-awk
+
+grep -v "#" "$1" | grep -v "@" > tempone.txt
+grep -v "#" "$2" | grep -v "@" > temptwo.txt
+awk 'FNR==NR{a[NR]=$1;next}{$1=a[FNR]}1' temptwo.txt tempone.txt

utils/bash-xvg-plugin/tests/__init__.py

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+"""Tests for bash_xvg."""

utils/bash-xvg-plugin/tests/rmsd1.xvg

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+# This file was created Wed May 15 18:52:40 2024
+# Created by:
+#                 :-) GROMACS - gmx rms, 2022.2-conda_forge (-:
+#
+# Executable:   /usr/local/bin.AVX2_256/gmx
+# Data prefix:  /usr/local
+# Working dir:  /jAiJpn
+# Command line:
+#   gmx rms -fit none -n /var/lib/cwl/stg854534b4-dcba-4641-a8e0-289ad164dad7/MOL.ndx -s /var/lib/cwl/stg2e049b7d-2261-481a-8b2e-f87a749a2820/complex.gro -f /var/lib/cwl/stg728ca10c-9429-421c-87f5-a5da2d92df29/prod_align_protein_ca.pdb -o rmsd_equil_ligand_notime.xvg
+# gmx rms is part of G R O M A C S:
+#
+# GROningen MAchine for Chemical Simulation
+#
+@    title "RMSD"
+@    xaxis  label "Time (ps)"
+@    yaxis  label "RMSD (nm)"
+@TYPE xy
+@ subtitle "resname_MOL after no fit"
+   0.0000000    0.0005156
+   0.0000000    0.0296825
+   0.0000000    0.0469071
+   0.0000000    0.0253868
+   0.0000000    0.0279059
+   0.0000000    0.0438598
+   0.0000000    0.0250407
+   0.0000000    0.0494208
+   0.0000000    0.0510193
+   0.0000000    0.0347102

utils/bash-xvg-plugin/tests/rmsd2.xvg

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+# This file was created Wed May 15 18:52:40 2024
+# Created by:
+#                 :-) GROMACS - gmx rms, 2022.2-conda_forge (-:
+#
+# Executable:   /usr/local/bin.AVX2_256/gmx
+# Data prefix:  /usr/local
+# Working dir:  /jAiJpn
+# Command line:
+#   gmx rms -fit none -n /var/lib/cwl/stg854534b4-dcba-4641-a8e0-289ad164dad7/MOL.ndx -s /var/lib/cwl/stg2e049b7d-2261-481a-8b2e-f87a749a2820/complex.gro -f /var/lib/cwl/stg728ca10c-9429-421c-87f5-a5da2d92df29/prod_align_protein_ca.pdb -o rmsd_equil_ligand_notime.xvg
+# gmx rms is part of G R O M A C S:
+#
+# GROningen MAchine for Chemical Simulation
+#
+@    title "RMSD"
+@    xaxis  label "Time (ps)"
+@    yaxis  label "RMSD (nm)"
+@TYPE xy
+@ subtitle "resname_MOL after no fit"
+   0.0000000    0.0006156
+   0.0000000    0.0396825
+   0.0000000    0.0469065
+   0.0000000    0.0353868
+   0.0000000    0.0479059
+   0.0000000    0.0488598
+   0.0000000    0.0550407
+   0.0000000    0.0694208
+   0.0000000    0.0210193
+   0.0000000    0.0247102

utils/bash-xvg-plugin/tests/test_bash_xvg.py

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+"""Tests for bash_xvg."""
+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_bash_xvg() -> None:
+    """Test bash_xvg."""
+    cwl_file = Path("bash_xvg.cwl")
+    input_to_props = parse_cwl_arguments(cwl_file)
+
+    input_xvg1_path = "rmsd1.xvg"
+    input_xvg1_path = str(Path(__file__).resolve().parent / Path(input_xvg1_path))
+    input_to_props["input_xvg1_path"]["path"] = input_xvg1_path
+
+    input_xvg2_path = "rmsd2.xvg"
+    input_xvg2_path = str(Path(__file__).resolve().parent / Path(input_xvg2_path))
+    input_to_props["input_xvg2_path"]["path"] = input_xvg2_path
+
+    input_to_props["output_xvg_path"] = "output.xvg"
+    input_yaml_path = Path("bash_xvg.yml")
+    create_input_yaml(input_to_props, input_yaml_path)
+    call_cwltool(cwl_file, input_yaml_path)
+    assert Path("output.xvg").exists()