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comparison COBRAxy/docs/tools/ras-generator.md @ 542:fcdbc81feb45 draft

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author francesco_lapi
date Sun, 26 Oct 2025 19:27:41 +0000
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541:fa93040a75af 542:fcdbc81feb45
16 16
17 ### Required Parameters 17 ### Required Parameters
18 18
19 | Parameter | Short | Type | Description | 19 | Parameter | Short | Type | Description |
20 |-----------|--------|------|-------------| 20 |-----------|--------|------|-------------|
21 | `--tool_dir` | `-td` | string | COBRAxy installation directory |
22 | `--input` | `-in` | file | Gene expression dataset (TSV format) | 21 | `--input` | `-in` | file | Gene expression dataset (TSV format) |
23 | `--ras_output` | `-ra` | file | Output file for RAS values | 22 | `--ras_output` | `-ra` | file | Output file for RAS values |
24 | `--rules_selector` | `-rs` | choice | Built-in model (ENGRO2, Recon, HMRcore) | 23 | `--rules_selector` | `-rs` | choice | Built-in model (ENGRO2, Recon, HMRcore) |
25 24
26 ### Optional Parameters 25 ### Optional Parameters
27 26
28 | Parameter | Short | Type | Default | Description | 27 | Parameter | Short | Type | Default | Description |
29 |-----------|--------|------|---------|-------------| 28 |-----------|--------|------|---------|-------------|
29 | `--tool_dir` | `-td` | string | auto-detected | COBRAxy installation directory (automatically detected after pip install) |
30 | `--none` | `-n` | boolean | true | Handle missing gene values | 30 | `--none` | `-n` | boolean | true | Handle missing gene values |
31 | `--model_upload` | `-rl` | file | - | Custom GPR rules file | 31 | `--model_upload` | `-rl` | file | - | Custom GPR rules file |
32 | `--model_upload_name` | `-rn` | string | - | Custom model name | 32 | `--model_upload_name` | `-rn` | string | - | Custom model name |
33 | `--out_log` | - | file | log.txt | Output log file | 33 | `--out_log` | - | file | log.txt | Output log file |
34
35 > **Note**: After installing COBRAxy via pip, the `--tool_dir` parameter is automatically detected and doesn't need to be specified.
34 36
35 ## Input Format 37 ## Input Format
36 38
37 ### Gene Expression File 39 ### Gene Expression File
38 ```tsv 40 ```tsv
100 ## Usage Examples 102 ## Usage Examples
101 103
102 ### Command Line 104 ### Command Line
103 105
104 ```bash 106 ```bash
105 # Basic usage with built-in model 107 # Basic usage with built-in model (after pip install)
106 ras_generator -td /path/to/COBRAxy \ 108 ras_generator \
107 -in expression_data.tsv \ 109 -in expression_data.tsv \
108 -ra ras_output.tsv \ 110 -ra ras_output.tsv \
109 -rs ENGRO2 111 -rs ENGRO2
110 112
111 # With custom model and strict missing gene handling 113 # With custom model and strict missing gene handling
112 ras_generator -td /path/to/COBRAxy \ 114 ras_generator \
113 -in expression_data.tsv \ 115 -in expression_data.tsv \
114 -ra ras_output.tsv \ 116 -ra ras_output.tsv \
115 -rl custom_rules.tsv \ 117 -rl custom_rules.tsv \
116 -rn "CustomModel" \ 118 -rn "CustomModel" \
117 -n false 119 -n false
118 ``` 120
119 121 # Explicitly specify tool directory (only needed if not using pip install)
120 ### Python API 122 ras_generator -td /path/to/COBRAxy \
121 123 -in expression_data.tsv \
122 ```python 124 -ra ras_output.tsv \
123 import ras_generator 125 -rs ENGRO2
124
125 # Basic RAS generation
126 args = [
127 '-td', '/path/to/COBRAxy',
128 '-in', 'expression_data.tsv',
129 '-ra', 'ras_output.tsv',
130 '-rs', 'ENGRO2'
131 ]
132
133 ras_generator.main(args)
134 ``` 126 ```
135 127
136 ### Galaxy Usage 128 ### Galaxy Usage
137 129
138 1. Upload gene expression file to Galaxy 130 1. Upload gene expression file to Galaxy