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comparison COBRAxy/ras_to_bounds.xml @ 88:c5820d87b4a5 draft

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author luca_milaz
date Sun, 13 Oct 2024 11:33:51 +0000
parents 9c802c5cad40
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87:9c802c5cad40 88:c5820d87b4a5
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
32 #end if 33 #end if
33 --out_log $log 34 --out_log $log
34 ]]> 35 ]]>
35 </command> 36 </command>
36 <inputs> 37 <inputs>
46 <option value="True" selected="true">Yes</option> 47 <option value="True" selected="true">Yes</option>
47 <option value="False">No</option> 48 <option value="False">No</option>
48 </param> 49 </param>
49 <when value="True"> 50 <when value="True">
50 <param name="input_ras" argument="--input_ras" multiple="true" type="data" format="tabular, csv, tsv" label="RAS matrix:" /> 51 <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." />
51 </when> 53 </when>
52 </conditional> 54 </conditional>
53 55
54 <conditional name="cond_medium"> 56 <conditional name="cond_medium">
55 <expand macro="options_ras_to_bounds_medium"/> 57 <expand macro="options_ras_to_bounds_medium"/>
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. 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.
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. 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.
82 84
83 Accepted files: 85 Accepted files:
84 - A model: JSON or XML file reporting reactions and rules contained in the model. 86 - A model: JSON or XML file reporting reactions and rules contained in the model.
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. 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.
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.
86 - Medium: tab-separated file containing lower and upper-bounds of medium reactions. 89 - Medium: tab-separated file containing lower and upper-bounds of medium reactions.
87 90
88 Example of custum growth medium fileeeee: 91 Example of custum growth medium file:
89 92
90 93
91 +------------+----------------+----------------+ 94 +------------+----------------+----------------+
92 | Reaction ID| lower_bound | upper_bound | 95 | Reaction ID| lower_bound | upper_bound |
93 +============+================+================+ 96 +============+================+================+
95 +------------+----------------+----------------+ 98 +------------+----------------+----------------+
96 | r2 | 0.268765 | 0.765567 | 99 | r2 | 0.268765 | 0.765567 |
97 +------------+----------------+----------------+ 100 +------------+----------------+----------------+
98 101
99 102
100 Example for multiple RAS matrices:
101 - cancer.csv and normal.csv generated by RAS generator tool (the two class names are 'cancer' and 'normal').
102 - This tool returns one unique collection of bounds files for both cancer and normal cells (normalization is performed across all cells).
103 - The association cell-class is reported in the 'cell_class' file that is useful to perform flux enrichment analysis based on class partenrship.
104
105 Output: 103 Output:
106 ------------- 104 -------------
107 105
108 The tool generates: 106 The tool generates:
109 - bounds: reporting the bounds of the model, or cells if RAS is used. Format: tab-separated. 107 - bounds: reporting the bounds of the model, or cells if RAS is used. Format: tab-separated.
110 - 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. 108 - Classes: a file containing the class of each cell (only if multiple RAS matrices were uploaded). Format: tab-separated.
111 - a log file (.txt). 109 - a log file (.txt).
112 ]]> 110 ]]>
113 </help> 111 </help>
114 <expand macro="citations" /> 112 <expand macro="citations" />
115 </tool> 113 </tool>