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Correcting order of CLI arguments in README #48

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surajsept merged 3 commits into from
Jul 27, 2025
Merged

Correcting order of CLI arguments in README #48

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10127dc
correcting order of CLI arguments in README
Jul 27, 2025
dfdfc94
copilot suggested reorder
sauter-roland Jul 27, 2025
30b599d
inserting model file parameter for second CLI example call in README
Jul 27, 2025
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9 changes: 5 additions & 4 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -100,17 +100,18 @@ 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).
* `<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.

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>
```
* `<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.
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sauter-roland marked this conversation as resolved.
* `<condition_column_name>`: Name of the column with condition expression data.
Expand All @@ -119,7 +120,7 @@ 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)
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