Mercurial > repos > bimib > cobraxy

changeset 541:fa93040a75af draft default tip

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Uploaded
author francesco_lapi
date Sat, 25 Oct 2025 15:20:55 +0000
parents 7d5b35c715e8
children
files COBRAxy/src/importMetabolicModel.xml COBRAxy/src/marea_macros.xml
diffstat 2 files changed, 5 insertions(+), 4 deletions(-) [+]
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--- a/COBRAxy/src/importMetabolicModel.xml	Sat Oct 25 15:08:19 2025 +0000
+++ b/COBRAxy/src/importMetabolicModel.xml	Sat Oct 25 15:20:55 2025 +0000
@@ -1,4 +1,5 @@
 <tool id="importMetabolicModel" name="Import Metabolic Model" version="2.0.0">
+    <description>Import a tabular model from file format (SBML, JSON, MAT or YAML)</description>
 
 	<requirements>
         <requirement type="package" version="1.24.4">numpy</requirement>
@@ -114,7 +115,8 @@
     <![CDATA[
 Overview
 -------------
-This tool generates a Tabular file (.tabular) containing the main information of the metabolic model, starting -either from a built-in model or a user-provided model file. 
+This tool generates a tabular file (.tabular) containing the main information of the metabolic model, starting either from a built-in model or a user-provided model file. 
+
 For built-in models, users can select among different nutrient-informed variants (i.e., different media composition) and gene nomenclature formats.
 
 The generated tabular file can be used as input for tools Expression2RAS, Expression2RPS, RAS2Bounds, Flux Simulation and Export Metabolic Model - within the COBRAxy suite.
@@ -123,8 +125,7 @@
 -------------
 
 The tool has three input parameters:
-    - Model: a file containing metabolic information (reactions, metabolites, genes). Ready-to-use models are ENGRO2 and Recon3D.
-    The user can also upload a custom model (see TIP 1).
+    - Model: a file containing metabolic information (reactions, metabolites, genes). Ready-to-use models are ENGRO2 and Recon3D. The user can also upload a custom model (see TIP 1).
     - Medium: choose a growth medium typically used for cell culture (see TIP 2 & 3). 
     - Gene nomenclature format: use the original GPR gene names or translate them into another nomenclature.
 
--- a/COBRAxy/src/marea_macros.xml	Sat Oct 25 15:08:19 2025 +0000
+++ b/COBRAxy/src/marea_macros.xml	Sat Oct 25 15:20:55 2025 +0000
@@ -237,7 +237,7 @@
                 @article{damiani2025Integrated,
                 title={Integrated enrichment and visualisation of metabolomics and transcriptomics with Galaxy},
                 author={Lapi, Francesco and Turati, Matteo and Ferrari, Michele and Fassi, Valerio and Vanoni, Marco and Galuzzi, Bruno G and Damiani, Chiara},
-                journal={},
+                journal={UNDER PRESS},
                 volume={},
                 pages={},
                 year={2025},