# HG changeset patch # User tduigou # Date 1682903954 0 # Node ID ada9a9847d10b7e9a457015bd9c6044567aafa0a # Parent 71ee7ebb4a6773e709225026689d1da2302b657c planemo upload for repository https://github.com/brsynth/rrparser commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6 diff -r 71ee7ebb4a67 -r ada9a9847d10 LICENSE --- a/LICENSE Mon Apr 03 12:45:49 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ -MIT License - -Copyright (c) 2020 Jean-Loup Faulon's group & INRA -Copyright (c) 2020 University of Evry / Paris-Saclay - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. diff -r 71ee7ebb4a67 -r ada9a9847d10 README.md --- a/README.md Mon Apr 03 12:45:49 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,71 +0,0 @@ -# RRulesParser Galaxy wrapper - -The open-source software package RRulesParser is available here : https://github.com/brsynth/RRParser - -## Installing - -* Create a new section in the Galaxy config file `config/tool_conf.xml` and paste the following: -``` -

- -

-``` - -* Make sure that the following entry exists under Galaxy's destination tag in `config/job_conf.xml`: -``` - -``` - -And that the destination of the tool is referred under the tools tag in `config/job_conf.xml`: - -``` - -``` - -## How to run RRulesParser wrapper tests - -In order to execute tests on RRulesParser wrapper, you need to: - - - Connect to your galaxy instance in interactive mode: - - ```bash - docker exec -it -u root galaxy_galaxy_1 bash - ``` - - Copy all the contents of `test-data` folder into your own test-data directory which is located in your local galaxy instance : `/galaxy/test-data`. It contains all the input files and expected output files needed for the tests. - - - Install Planemo: - You can see here the documentation for Planemo Installation : https://planemo.readthedocs.io/en/latest/installation.html - Note that they recommand to install Planemo by setting up a virtual environment: - - ```bash - python3 -m venv planemo - . planemo/bin/activate - pip install -U planemo - ``` - - Upgrade pip if needed. - - - run the tests: - - ```bash - planemo test --conda_channels conda-forge tools/synbiocad-galaxy-wrappers/RRulesParser/wrap.xml --biocontainers --no_conda_auto_init - ``` - - IMPORTANT: Maybe you will need to remove CONDA from your PATH for the command `planemo test` to run correctly. To do that, you can edit this file `~/.bashrc`, comment this line `PATH="/root/anaconda3/bin:$PATH"` and save changes. - - Planemo will output an html test summary `tool_test_output.html`. - -## Built With - -* [Galaxy](https://galaxyproject.org) - The Galaxy project - - -## Authors - -* Melchior du Lac -* Joan Hérisson -* Thomas Duigou - -## License - -This project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details diff -r 71ee7ebb4a67 -r ada9a9847d10 rrparser.xml --- a/rrparser.xml Mon Apr 03 12:45:49 2023 +0000 +++ b/rrparser.xml Mon May 01 01:19:14 2023 +0000 @@ -38,6 +38,9 @@ + + + @@ -109,6 +112,6 @@ - 10.1093/nar/gky940 + 10.1093/nar/gky940