From 10127dc869ed515d4b21f1561c85bd5320625578 Mon Sep 17 00:00:00 2001
From: Roland Sauter <sauter.roland@pm.me>
Date: Sun, 27 Jul 2025 15:50:56 +0200
Subject: [PATCH 1/3] correcting order of CLI arguments in README

---
 README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index eecb391..a1bd5d3 100644
--- a/README.md
+++ b/README.md
@@ -100,7 +100,7 @@ The CLI allows you to calculate differential centralities using gene expression
 
 1.  **Using a single file with pre-calculated fold-changes:**
     ```bash
-    gemcat <expression_file.csv> <model_file.xml> -e <column_name> -o <result_file.csv>
+    gemcat <model_file.xml> <expression_file.csv> -e <column_name> -o <result_file.csv>
     ```
     * `<expression_file.csv>`: Path to your input file.
     * `<model_file.xml>`: Path to your metabolic model file (SBML, JSON, or MAT format).
@@ -109,7 +109,7 @@ The CLI allows you to calculate differential centralities using gene expression
 
 2.  **Using two files (or one) with condition and baseline expression values:**
     ```bash
-    gemcat <condition_file.csv> <model_file.xml> -e <condition_column_name> -b <baseline_file.csv> -c <baseline_column_name> -o <result_file.csv>
+    gemcat <model_file.xml> <condition_file.csv> -e <condition_column_name> -b <baseline_file.csv> -c <baseline_column_name> -o <result_file.csv>
     ```
     * `<condition_file.csv>`: Path to the file with expression values for your experimental condition.
     * `<baseline_file.csv>`: Path to the file with baseline expression values. If this is the same as the condition file, you can omit the `-b` flag and just use `<condition_file.csv>` as the second positional argument.
@@ -119,7 +119,7 @@ The CLI allows you to calculate differential centralities using gene expression
 3.  **Using built-in models:**
     If you don't have a model file, GEMCAT can automatically access some common models by name:
     ```bash
-    gemcat <expression_file.csv> <model_name> -e <column_name> -o <result_file.csv>
+    gemcat <model_name> <expression_file.csv> -e <column_name> -o <result_file.csv>
     ```
     Currently supported model names:
     * `recon3d`: [Recon3D](http://bigg.ucsd.edu/models/Recon3D)

From dfdfc940d50adf3030b8fb270d084d8ecff8d1ac Mon Sep 17 00:00:00 2001
From: sauter-roland <sauter.roland@googlemail.com>
Date: Sun, 27 Jul 2025 16:11:58 +0200
Subject: [PATCH 2/3] copilot suggested reorder

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index a1bd5d3..ad55ac0 100644
--- a/README.md
+++ b/README.md
@@ -102,8 +102,8 @@ The CLI allows you to calculate differential centralities using gene expression
     ```bash
     gemcat <model_file.xml> <expression_file.csv> -e <column_name> -o <result_file.csv>
     ```
-    * `<expression_file.csv>`: Path to your input file.
     * `<model_file.xml>`: Path to your metabolic model file (SBML, JSON, or MAT format).
+    * `<expression_file.csv>`: Path to your input file.
     * `<column_name>`: The name of the column in your CSV containing the fold-change values.
     * `<result_file.csv>`: The desired output file path.
 

From 30b599db988b741965ef098739e619bd3883676b Mon Sep 17 00:00:00 2001
From: Roland Sauter <sauter.roland@pm.me>
Date: Sun, 27 Jul 2025 16:15:00 +0200
Subject: [PATCH 3/3] inserting model file parameter for second CLI example
 call in README

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index ad55ac0..59acd41 100644
--- a/README.md
+++ b/README.md
@@ -111,6 +111,7 @@ The CLI allows you to calculate differential centralities using gene expression
     ```bash
     gemcat <model_file.xml> <condition_file.csv> -e <condition_column_name> -b <baseline_file.csv> -c <baseline_column_name> -o <result_file.csv>
     ```
+    * `<model_file.xml>`: Path to your metabolic model file (SBML, JSON, or MAT format).
     * `<condition_file.csv>`: Path to the file with expression values for your experimental condition.
     * `<baseline_file.csv>`: Path to the file with baseline expression values. If this is the same as the condition file, you can omit the `-b` flag and just use `<condition_file.csv>` as the second positional argument.
     * `<condition_column_name>`: Name of the column with condition expression data.