# 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.-])*$ - +