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comparison COBRAxy/ras_to_bounds.xml @ 59:d4162562c8f5 draft

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Uploaded
author luca_milaz
date Sun, 13 Oct 2024 07:20:51 +0000
parents 4f11c68210a7
children c46df775b9fa
comparison
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58:42a8ccae86cd 59:d4162562c8f5
27 --medium $medium 27 --medium $medium
28 #end if 28 #end if
29 --ras_selector $cond_ras.ras_choice 29 --ras_selector $cond_ras.ras_choice
30 #if $cond_ras.ras_choice == "True" 30 #if $cond_ras.ras_choice == "True"
31 --input_ras $cond_ras.input_ras 31 --input_ras $cond_ras.input_ras
32 --classes $cond_ras.classes
33 #end if 32 #end if
34 --out_log $log 33 --out_log $log
35 ]]> 34 ]]>
36 </command> 35 </command>
37 <inputs> 36 <inputs>
47 <option value="True" selected="true">Yes</option> 46 <option value="True" selected="true">Yes</option>
48 <option value="False">No</option> 47 <option value="False">No</option>
49 </param> 48 </param>
50 <when value="True"> 49 <when value="True">
51 <param name="input_ras" argument="--input_ras" multiple="true" type="data" format="tabular, csv, tsv" label="RAS matrix:" /> 50 <param name="input_ras" argument="--input_ras" multiple="true" type="data" format="tabular, csv, tsv" label="RAS matrix:" />
52 <param name="classes" argument="--classes" type="text" value="None" label="Classes:" help="Write here the the classes to assign to each of the uploaded RAS matrices. Example for two RAS matrices:'cellNormal, cellCancer'. If you uploaded just one matrix, leave default value." />
53 </when> 51 </when>
54 </conditional> 52 </conditional>
55 53
56 <conditional name="cond_medium"> 54 <conditional name="cond_medium">
57 <expand macro="options_ras_to_bounds_medium"/> 55 <expand macro="options_ras_to_bounds_medium"/>
82 Moreover, it enables to use custom/pre-defined growth mediums to constrain exchange reactions. For a custom medium, It is suggested to use the template file returned by the Custom Data Generator tool. 80 Moreover, it enables to use custom/pre-defined growth mediums to constrain exchange reactions. For a custom medium, It is suggested to use the template file returned by the Custom Data Generator tool.
83 If the RAS matrix, generated by the RAS generator tool, is used, then a bounds file is generated for each cell. Otherwise, a single bounds file is returned. 81 If the RAS matrix, generated by the RAS generator tool, is used, then a bounds file is generated for each cell. Otherwise, a single bounds file is returned.
84 82
85 Accepted files: 83 Accepted files:
86 - A model: JSON or XML file reporting reactions and rules contained in the model. 84 - A model: JSON or XML file reporting reactions and rules contained in the model.
87 - RAS matrix: tab-separated RAS file as returned by RAS generator. It can be a collection of RAS files too (e.g. one RAS matrix for normal cells and one for cancer cells). Note that if multiple RAs matrices are uploaded, the bounds are normalzed across all cells. 85 - RAS matrix: tab-separated RAS file as returned by RAS generator. Multiple RAS files can be uploaded too (e.g. one RAS matrix for normal cells and one for cancer cells). Note that if multiple RAs matrices are uploaded, the bounds are normalzed across all cells.
88 - Classes: If multiple RAS matrices are uploaded, then the tool returns a simple file containing for each cell the class it belongs to (cells coming from the same RAS matrix are assigned to the same class). This file is useful in the Flux enrichment analysis tool.
89 - Medium: tab-separated file containing lower and upper-bounds of medium reactions. 86 - Medium: tab-separated file containing lower and upper-bounds of medium reactions.
90 87
91 Example of custum growth medium file: 88 Example of custum growth medium file:
92 89
93 90
97 | r1 | 0.123167 | 0.371355 | 94 | r1 | 0.123167 | 0.371355 |
98 +------------+----------------+----------------+ 95 +------------+----------------+----------------+
99 | r2 | 0.268765 | 0.765567 | 96 | r2 | 0.268765 | 0.765567 |
100 +------------+----------------+----------------+ 97 +------------+----------------+----------------+
101 98
99 Example for multiple RAS matrices:
100 - cancer.csv and normal.csv generated by RAS generator tool (the two class names are 'cancer' and 'normal').
101 - This tool returns one unique collection of bounds files for both cancer and normal cells (normalization is performed across all cells).
102 - The association cell-class is reported in the 'cell_class' file that is udesul to perform flux enrichment analysis based on class partenrship.
102 103
103 Output: 104 Output:
104 ------------- 105 -------------
105 106
106 The tool generates: 107 The tool generates:
107 - bounds: reporting the bounds of the model, or cells if RAS is used. Format: tab-separated. 108 - bounds: reporting the bounds of the model, or cells if RAS is used. Format: tab-separated.
108 - Classes: a file containing the class of each cell (only if multiple RAS matrices were uploaded). Format: tab-separated. 109 - Classes: a file containing the class of each cell (only if multiple RAS matrices were uploaded). The class name of a RAS matrix corresponds to its file name. Format: tab-separated.
109 - a log file (.txt). 110 - a log file (.txt).
110 ]]> 111 ]]>
111 </help> 112 </help>
112 <expand macro="citations" /> 113 <expand macro="citations" />
113 </tool> 114 </tool>