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README.md

cwl2argparse

cwl2argparse generates an argparse definition from CWL tool arguments that can be pasted in a Python program and used

search.cwl

#!/usr/bin/env cwl-runner
cwlVersion: "cwl:draft-3"
class: CommandLineTool
baseCommand: ['search.py']

description: |
  Toy program to search inverted index and print out each line the term appears
inputs:
  - id: mainfile
  type: File
  description: Text file to be indexed
  inputBinding:
    position: 1

- id: term
  type: string
  description: Term for search
  inputBinding:
    position: 2

outputs:
    []

Result search.py

import argparse


def parser():
    description="""
        Toy program to search inverted index and print out each line the term appears
    """
    
    parser = argparse.ArgumentParser(description=description)
    arg_mainfile = parser.add_argument("arg_mainfile",
        type=argparse.FileType(),       help="""Text file to be indexed""",)
    arg_term = parser.add_argument("arg_term",
        type=str,       help="""Term for search""",)

    return parser

Installation

$ pip install cwl2argparse

Running

cwl2argparse FILES [FILES ...] [options]

Options:

  • FILES - a list of CWL tool descriptions or directories with tools
  • -p, --prefix - Prefix to be added to all argument variables in resulting Python code.

For instance, providing arg_ as a prefix will result in generating the next lines for the example above:

    arg_mainfile = parser.add_argument("mainfile",
        type=argparse.FileType(),help="""Text file to be indexed""",)
    arg_term = parser.add_argument("term",
        type=str,help="""Term for search""",)
  • -d, --dest - Destination directory to store resulting .py files
  • -q, --quiet - Do not print generated code to system output
  • -y - If a file with a name the same as the generated one already exists, replace it without confirmation

About

cwl2argparse generates an argparse definition from CWL tool arguments that can be pasted in a Python program and used

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