--- 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.

--- 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:
-```
-<section id="sbc-rs" name="SynBioCAD RetroSynthesis">
-    <tool file="synbiocad-galaxy-wrappers/RRulesParser/wrap.xml" />
-</section>
-```
-
-* Make sure that the following entry exists under Galaxy's destination tag in `config/job_conf.xml`:
-```
-<destination id="local" runner="local" />
-```
-
-And that the destination of the tool is referred under the tools tag in `config/job_conf.xml`:
-
-```
-<tool id="RRulesParser" destination="local" />
-```
-
-## 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

--- 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 @@
                 <option value="all">RetroRules (all)</option>
                 <option value="rules-file">Other reaction rules...</option>
             </param>
+            <when value="retro"/>
+            <when value="forward"/>
+            <when value="all"/>
             <when value="rules-file">
                 <param name="file" type="data" format="csv" optional="False" label="Rules File" help="Filename of reaction rules"/>
                 <param name="input_format" type="select" optional="False" label="File format" help="Input file format (default: csv)">
@@ -109,6 +112,6 @@
         <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
     </creator>
     <citations>
-        <citation type="doi">10.1093/nar/gky940 </citation>
+        <citation type="doi">10.1093/nar/gky940</citation>
     </citations>
 </tool>