# HG changeset patch
# User ggricourt
# Date 1645195629 0
# Node ID 7f6f0555dad88bf7c5c3f645e3a773cba92c71da
# Parent 9142d12aa3a9d26cdf1ceea39b010818a47ee465
"planemo upload for repository https://github.com/brsynth/rpFbaAnalysis commit ef23da34410d659cc17ac08a60194f59bb1a9f3c-dirty"
diff -r 9142d12aa3a9 -r 7f6f0555dad8 README
--- a/README Fri Feb 11 16:10:33 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-# rpFbaAnalysis -- Run OptGene, OptKnock with an heterologous pathway
-
-The open-source software package rpFbaAnalysis is available here : https://github.com/brsynth/rptools/tree/master/rptools/rpFbaAnalysis
-
-## How to run rpFbaAnalysis wrapper tests
-
-In order to execute tests on rpFbaAnalysis 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 --conda_debug tools/BRSynthTools/rpFbaAnalysis/wrap.xml
- ```
-
- 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:$PATH"` and save changes.
-
- Planemo will output an html test summary `tool_test_output.html`.
diff -r 9142d12aa3a9 -r 7f6f0555dad8 wrap.xml
--- a/wrap.xml Fri Feb 11 16:10:33 2022 +0000
+++ b/wrap.xml Fri Feb 18 14:47:09 2022 +0000
@@ -24,8 +24,8 @@
--strategy '$input_strategy.strategy'
#if str($input_strategy.strategy) == "ko":
--substrate-rxn-id '$input_strategy.substrate_rxn_id'
- #if $input_strategy.email:
- --email '$input_strategy.email'
+ #if $input_strategy.annotate:
+ --email "$__user_email__"
#end if
#end if
--max-knockouts '$max_knockouts'
@@ -39,9 +39,11 @@
+ ^(?:[a-zA-Z_])(?:[\w.-])*$
+ ^(?:[a-zA-Z_])(?:[\w.-])*$
@@ -51,8 +53,9 @@
+ ^(?:[a-zA-Z_])(?:[\w.-])*$
-
+