Vcf2maf

.editorconfig

@@ -0,0 +1,21 @@
+# http://editorconfig.org
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+insert_final_newline = true
+charset = utf-8
+end_of_line = lf
+
+[*.bat]
+indent_style = tab
+end_of_line = crlf
+
+[LICENSE]
+insert_final_newline = false
+
+[Makefile]
+indent_style = tab

.gitbook.yaml

@@ -0,0 +1 @@
+root: ./docs

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,15 @@
+* cwl-commandlinetools version:
+* Python version:
+* Operating System:
+
+### Description
+
+Describe what you were trying to get done.
+Tell us what happened, what went wrong, and what you expected to happen.
+
+### What I Did
+
+```
+Paste the command(s) you ran and the output.
+If there was a crash, please include the traceback here.
+```

.gitignore

@@ -8,6 +8,7 @@ __pycache__/
 
 # Distribution / packaging
 .Python
+env/
 build/
 develop-eggs/
 dist/
@@ -81,8 +82,10 @@ celerybeat-schedule
 # SageMath parsed files
 *.sage.py
 
-# Environments
+# dotenv
 .env
+
+# virtualenv
 .venv
 env/
 venv/
@@ -108,7 +111,6 @@ venv.bak/
 
 # vscode
 .vscode/*
-!.vscode/settings.json
-!.vscode/tasks.json
-!.vscode/launch.json
-!.vscode/extensions.json
+
+# pycharm
+.idea

.travis.yml

@@ -0,0 +1,31 @@
+# Config file for automatic testing at travis-ci.org
+
+language: python
+python:
+  - 3.7
+  - 2.7
+
+# Command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
+install: 
+  - pip install -U tox-travis
+  - pip install -r requirements.txt
+
+# Command to run tests, e.g. python setup.py test
+script:
+  - find . -name '*.cwl' | xargs -n 1 cwltool --validate
+
+# Assuming you have installed the travis-ci CLI tool, after you
+# create the Github repo and add it to Travis, run the
+# following command to finish PyPI deployment setup:
+# $ travis encrypt --add deploy.password
+deploy:
+  provider: pypi
+  distributions: sdist bdist_wheel
+  user: __token__
+  password:
+    secure: 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
+  on:
+    tags: true
+    repo: msk-access/cwl-commandlinetools
+    python: 2.7
+

LICENSE

@@ -0,0 +1,16 @@
+Apache Software License 2.0
+
+Copyright (c) 2019, msk-access
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+

MANIFEST.in

@@ -0,0 +1,9 @@
+include LICENSE
+include README.md
+
+recursive-include tests *
+recursive-include *.cwl
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+recursive-include docs *.jpg *.png *.gif

Makefile

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+.PHONY: clean clean-test clean-pyc clean-build docs help
+.DEFAULT_GOAL := help
+
+define BROWSER_PYSCRIPT
+import os, webbrowser, sys
+
+try:
+	from urllib import pathname2url
+except:
+	from urllib.request import pathname2url
+
+webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
+endef
+export BROWSER_PYSCRIPT
+
+define PRINT_HELP_PYSCRIPT
+import re, sys
+
+for line in sys.stdin:
+	match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
+	if match:
+		target, help = match.groups()
+		print("%-20s %s" % (target, help))
+endef
+export PRINT_HELP_PYSCRIPT
+
+BROWSER := python -c "$$BROWSER_PYSCRIPT"
+
+help:
+	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
+
+clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
+
+clean-build: ## remove build artifacts
+	rm -fr build/
+	rm -fr dist/
+	rm -fr .eggs/
+	find . -name '*.egg-info' -exec rm -fr {} +
+	find . -name '*.egg' -exec rm -f {} +
+
+clean-pyc: ## remove Python file artifacts
+	find . -name '*.pyc' -exec rm -f {} +
+	find . -name '*.pyo' -exec rm -f {} +
+	find . -name '*~' -exec rm -f {} +
+	find . -name '__pycache__' -exec rm -fr {} +
+
+clean-test: ## remove test and coverage artifacts
+	rm -fr .tox/
+	rm -f .coverage
+	rm -fr htmlcov/
+	rm -fr .pytest_cache
+
+lint: ## check style with flake8
+	flake8 cwl_commandlinetools tests
+
+test: ## run tests quickly with the default Python
+	pytest
+
+test-all: ## run tests on every Python version with tox
+	tox
+
+coverage: ## check code coverage quickly with the default Python
+	coverage run --source cwl_commandlinetools -m pytest
+	coverage report -m
+	coverage html
+	$(BROWSER) htmlcov/index.html
+
+release: dist ## package and upload a release
+	twine upload dist/*
+
+dist: clean ## builds source and wheel package
+	python setup.py sdist
+	python setup.py bdist_wheel
+	ls -l dist
+
+install: clean ## install the package to the active Python's site-packages
+	python setup.py install

README.md

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+---
+description: Central location for storing common workflow language based command line tools for building workflows
+---
+
+# Command-line tools built by CCI
+
+- Free software: Apache Software License 2.0
+* Documentation: [https://msk-access.gitbook.io/command-line-tools-cwl/](https://msk-access.gitbook.io/command-line-tools-cwl/)
+
+## Features
+
+Create command line tools in common workflow language to generate workflows.
+
+## Installation
+
+Clone the repository:
+
+```
+git clone --depth 50 https://github.com/msk-access/cwl-commandlinetools.git
+```
+
+**Follow the README in respective tool folder for execution of the tool.**
+
+
+## Credits
+
+- CMO ACCESS Informatics Team
+- This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
+  - Cookiecutter: https://github.com/audreyr/cookiecutter
+  - `audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
+