changeset 2:7f6f0555dad8 draft

"planemo upload for repository https://github.com/brsynth/rpFbaAnalysis commit ef23da34410d659cc17ac08a60194f59bb1a9f3c-dirty"

--- 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`.

--- 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 @@
 
         <param name="biomass_rxn_id" type="text" label="Biomass reaction ID" value="" >
             <validator type="empty_field" message="Biomass reaction ID is required"/>
+            <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator>
         </param>
         <param name="target_rxn_id" type="text" label="Target reaction ID" value="" >
             <validator type="empty_field" message="Target reaction ID is required"/>
+            <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator>
         </param>
         <conditional name="input_strategy">
             <param name="strategy" type="select" label="Strategy">
@@ -51,8 +53,9 @@
             <when value="ko">
                 <param name="substrate_rxn_id" type="text" label="Substrate reaction ID" value="" >
                     <validator type="empty_field" message="Substrate reaction ID is required"/>
+                    <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator>
                 </param>
-                <param name="email" type="text" label="Email" value=""/>
+                <param name="annotate" type="boolean" label="Annotate the genes" checked="false" help="Your address mail will be use to query the NCBI website with biopython" />
             </when>
             <when value="ou">
             </when>