# HG changeset patch
# User tduigou
# Date 1680521838 0
# Node ID dd0dfd2cb8a833c8ac9edd71c22d26b4233e3bc6
# Parent  092545561208e33abf3fa2fc953bb2594b0caabc
planemo upload commit 9c19f737cd6e2152151c8bf97a53ab1afe51a4a0

diff -r 092545561208 -r dd0dfd2cb8a8 LICENSE
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE	Mon Apr 03 11:37:18 2023 +0000
@@ -0,0 +1,22 @@
+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 092545561208 -r dd0dfd2cb8a8 README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Mon Apr 03 11:37:18 2023 +0000
@@ -0,0 +1,71 @@
+# 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:$PATH"` and save changes.
+
+  Planemo will output an html test summary `tool_test_output.html`.
+
+## Built With
+
+* [Galaxy](https://galaxyproject.org) - The Galaxy project
+
+
+## Authors
+
+* Melchior du Lac
+* Joan Hérisson
+* Thomas Duigou
+
+## License
+
+This project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details
diff -r 092545561208 -r dd0dfd2cb8a8 config/job_conf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/config/job_conf.xml	Mon Apr 03 11:37:18 2023 +0000
@@ -0,0 +1,1 @@
+    <tool id="rrparser" destination="local" />
diff -r 092545561208 -r dd0dfd2cb8a8 config/tool_conf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/config/tool_conf.xml	Mon Apr 03 11:37:18 2023 +0000
@@ -0,0 +1,3 @@
+  <section id="sbc-rs" name="SynBioCAD RetroSynthesis">
+    <tool file="synbiocad-galaxy-wrappers/rrparser/rrparser.xml" />
+  </section>
diff -r 092545561208 -r dd0dfd2cb8a8 rrparser.xml
--- a/rrparser.xml	Tue Jun 21 14:40:08 2022 +0000
+++ b/rrparser.xml	Mon Apr 03 11:37:18 2023 +0000
@@ -2,7 +2,7 @@
     <description>Retrieve the reaction rules from RetroRules</description>
     <macros>
         <token name="@VERSION_SUFFIX@">0</token>
-        <token name="@TOOL_VERSION@">2.4.6</token>
+        <token name="@TOOL_VERSION@">2.5.0</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">rrparser</requirement>
@@ -14,14 +14,15 @@
     <command detect_errors="exit_code"><![CDATA[
         python -m rrparser
         #if str($rules.type) != "rules-file":
-            retrorules
+            --rules_file retrorules
             --rule-type '$rules.type'
         #else:
-            '$rules.file'
+            --rules_file '$rules.file'
             --input-format '$rules.input_format'
         #end if
         --diameters '$diameters'
         --output-format csv
+        --rules-dir "\${TMPDIR:-.}"
         #if str($compress) == "true":
             --outfile '$out_rules'.csv.gz
             && mv '$out_rules'.csv.gz '$out_rules'
@@ -107,7 +108,7 @@
 Version
 -------
 
-v2.4.6
+v2.5.0
 
 Authors
 -------