Mercurial > repos > tduigou > get_sbml_model

changeset 1:ceffb29b60c9 draft

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planemo upload commit 9c19f737cd6e2152151c8bf97a53ab1afe51a4a0
author tduigou
date Mon, 03 Apr 2023 09:18:22 +0000
parents 4797d0b36ff3
children fa893f77dc22
files LICENSE README.md config/job_conf.xml config/tool_conf.xml get_infos.py get_sbml_model.xml
diffstat 6 files changed, 117 insertions(+), 30 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE	Mon Apr 03 09:18:22 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.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Mon Apr 03 09:18:22 2023 +0000
@@ -0,0 +1,32 @@
+# get_sbml_model - Pick an SBML model among a list
+
+## How to run get_sbml_model wrapper tests
+
+In order to execute tests on get_sbml_model 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
+  ```
+
+  - run the tests:
+
+  ```bash
+  planemo test tools/synbiocad-galaxy-wrappers/get_sbml_model/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`.
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/config/job_conf.xml	Mon Apr 03 09:18:22 2023 +0000
@@ -0,0 +1,1 @@
+    <tool id="get_sbml_model" destination="local" />
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/config/tool_conf.xml	Mon Apr 03 09:18:22 2023 +0000
@@ -0,0 +1,3 @@
+  <section id="sbc-util" name="SynBioCAD Utilities">
+    <tool file="synbiocad-galaxy-wrappers/get_sbml_model/get_sbml_model.xml" />
+  </section>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_infos.py	Mon Apr 03 09:18:22 2023 +0000
@@ -0,0 +1,44 @@
+from argparse import ArgumentParser
+from libsbml import (
+    readSBMLFromFile
+)
+
+
+def entry_point():
+    parser = ArgumentParser('Returns cell informations')
+    parser.add_argument(
+        'infile',
+        type=str,
+        help='SBML input file (xml)'
+    )
+    parser.add_argument(
+        '--comp',
+        type=str,
+        help='Path to store cell compartments'
+    )
+    parser.add_argument(
+        '--biomass',
+        type=str,
+        help='Path to store biomass reaction ID'
+    )
+    params = parser.parse_args()
+
+    sbml_doc = readSBMLFromFile(params.infile)
+
+    if params.comp:
+        compartments = sbml_doc.getModel().getListOfCompartments()
+        with open(params.comp, 'w') as f:
+            f.write('#ID\tNAME\n')
+            for comp in compartments:
+                f.write(f'{comp.getId()}\t{comp.getName()}\n')
+
+    if params.biomass:
+        reactions = sbml_doc.getModel().getListOfReactions()
+        with open(params.biomass, 'w') as f:
+            f.write('#ID\n')
+            for rxn in reactions:
+                if 'biomass' in rxn.getId().lower():
+                    f.write(f'{rxn.getId()}\n')
+
+if __name__ == "__main__":
+    entry_point()
\ No newline at end of file
--- a/get_sbml_model.xml	Tue Jan 11 16:17:26 2022 +0000
+++ b/get_sbml_model.xml	Mon Apr 03 09:18:22 2023 +0000
@@ -1,12 +1,14 @@
-<tool id="get_sbml_model" name="Pick SBML Model" version="0.0.1" profile="19.09">
-    <description>Pick an SBML model among a list</description>
+<tool id="get_sbml_model" name="Pick SBML Model" version="0.0.2" profile="19.09" license="MIT">
+    <description>Get an SBML model (BiGG)</description>
     <requirements>
         <requirement type="package" version="7.81.0">curl</requirement>
         <requirement type="package" version="1.11">gzip</requirement>
+        <requirement type="package" version="5.19.2">python-libsbml</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         curl -o - 'http://bigg.ucsd.edu/static/models/$(input).xml.gz'
-        | gunzip > '$sbml_model'
+        | gunzip > '$model';
+        python '$__tool_directory__/'get_infos.py '$model' --comp '$compartments' --biomass '$biomass'
     ]]></command>
     <inputs>
         <param name="input" type="select" label="Strain">
@@ -60,13 +62,17 @@
         </param>
     </inputs>
     <outputs>
-        <data name="sbml_model" format="xml" label="${tool.name} - ${input}" />
+        <data name="model" format="sbml" label="${input}" />
+        <data name="compartments" format="tsv" label="${input} (compartments)" />
+        <data name="biomass" format="tsv" label="${input} (biomass reactions)" />
     </outputs>
     <tests>
         <test>
         <!-- test 1: check if identical outputs are produced with iML1515 model input  -->
             <param name="input" value="iML1515" />
-            <output name="sbml_model" md5="9bf81d20cab5476700697ded95b716d1"/>
+            <output name="model" md5="9bf81d20cab5476700697ded95b716d1"/>
+            <output name="comp" md5="e93a875a2d8efc10a880ae3ac0018236"/>
+            <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -74,29 +80,8 @@
 =================
 
 Download the selected SBML model fromg BiGG database.
-
-
-Version
-----------
-0.0.1
-
-
-Authors
--------
-
-* Joan Hérisson
-
-
-License
--------
-
-`MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
-
-
-Acknowledgments
----------------
-
-* Kenza Bazi-Kabbaj
-
     ]]></help>
-</tool>
\ No newline at end of file
+    <creator>
+        <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
+    </creator>
+</tool>