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comparison COBRAxy/ras_to_bounds.xml @ 49:1552a2ddea58 draft

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author luca_milaz
date Sat, 12 Oct 2024 19:57:19 +0000
parents e962ba5fc27d
children fc411b10e419
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48:fac6930e6385 49:1552a2ddea58
15 <command detect_errors="exit_code"> 15 <command detect_errors="exit_code">
16 <![CDATA[ 16 <![CDATA[
17 python $__tool_directory__/ras_to_bounds.py 17 python $__tool_directory__/ras_to_bounds.py
18 --tool_dir $__tool_directory__ 18 --tool_dir $__tool_directory__
19 --model_selector $cond_model.model_selector 19 --model_selector $cond_model.model_selector
20 --cell_class $cell_class
21 --classes $classes
20 #if $cond_model.model_selector == 'Custom' 22 #if $cond_model.model_selector == 'Custom'
21 --model $model 23 --model $model
22 --model_name $model.element_identifier 24 --model_name $model.element_identifier
23 #end if 25 #end if
24 --medium_selector $cond_medium.medium_selector 26 --medium_selector $cond_medium.medium_selector
44 <param name="ras_choice" argument="--ras_choice" type="select" label="Do want to use RAS?"> 46 <param name="ras_choice" argument="--ras_choice" type="select" label="Do want to use RAS?">
45 <option value="True" selected="true">Yes</option> 47 <option value="True" selected="true">Yes</option>
46 <option value="False">No</option> 48 <option value="False">No</option>
47 </param> 49 </param>
48 <when value="True"> 50 <when value="True">
49 <param name="input_ras" argument="--input_ras" multiple="false" 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" 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, ignore this." />
50 </when> 53 </when>
51 </conditional> 54 </conditional>
52 55
53 <conditional name="cond_medium"> 56 <conditional name="cond_medium">
54 <expand macro="options_ras_to_bounds_medium"/> 57 <expand macro="options_ras_to_bounds_medium"/>
59 62
60 </inputs> 63 </inputs>
61 64
62 <outputs> 65 <outputs>
63 <data format="txt" name="log" label="RAStoBounds- Log" /> 66 <data format="txt" name="log" label="RAStoBounds- Log" />
64 67 <data format="tabular" name="cell_class" label="RAStoBounds - Cells class" />
65 <collection name="ras_to_bounds" type="list" label="Ras to Bounds"> 68 <collection name="ras_to_bounds" type="list" label="Ras to Bounds">
66 <discover_datasets name = "collection" pattern="__name_and_ext__" directory="ras_to_bounds"/> 69 <discover_datasets name = "collection" pattern="__name_and_ext__" directory="ras_to_bounds"/>
67 </collection> 70 </collection>
68 71
69 </outputs> 72 </outputs>
79 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.
80 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.
81 84
82 Accepted files: 85 Accepted files:
83 - 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.
84 - RAS matrix: tab-separated RAS file as returned by RAS generator. 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.
85 - 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.
86 90
87 Example of custum growth medium file: 91 Example of custum growth medium file:
88 92
89 93
99 Output: 103 Output:
100 ------------- 104 -------------
101 105
102 The tool generates: 106 The tool generates:
103 - 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.
108 - Classes: a file containing the class of each cell (only if multiple RAS matrices were uploaded). Format: tab-separated.
104 - a log file (.txt). 109 - a log file (.txt).
105 ]]> 110 ]]>
106 </help> 111 </help>
107 <expand macro="citations" /> 112 <expand macro="citations" />
108 </tool> 113 </tool>