4
+ − 1 <tool id="MaREA RAS to bounds" name="RAStoBounds" version="2.0.0">
+ − 2
+ − 3 <macros>
+ − 4 <import>marea_macros.xml</import>
+ − 5 </macros>
+ − 6
+ − 7 <requirements>
+ − 8 <requirement type="package" version="1.24.4">numpy</requirement>
+ − 9 <requirement type="package" version="2.0.3">pandas</requirement>
+ − 10 <requirement type="package" version="0.29.0">cobra</requirement>
+ − 11 <requirement type="package" version="5.2.2">lxml</requirement>
+ − 12 <requirement type="package" version="1.4.2">joblib</requirement>
+ − 13 </requirements>
+ − 14
+ − 15 <command detect_errors="exit_code">
+ − 16 <![CDATA[
+ − 17 python $__tool_directory__/ras_to_bounds.py
+ − 18 --tool_dir $__tool_directory__
+ − 19 --model_selector $cond_model.model_selector
+ − 20 #if $cond_model.model_selector == 'Custom'
+ − 21 --model $model
+ − 22 --model_name $model.element_identifier
+ − 23 #end if
+ − 24 --medium_selector $cond_medium.medium_selector
+ − 25 #if $cond_medium.medium_selector == 'Custom'
+ − 26 --medium $medium
+ − 27 #end if
+ − 28 --ras_selector $cond_ras.ras_choice
+ − 29 #if $cond_ras.ras_choice == "True"
+ − 30 --input_ras $cond_ras.input_ras
+ − 31 #end if
+ − 32 --out_log $log
+ − 33 ]]>
+ − 34 </command>
+ − 35 <inputs>
+ − 36 <conditional name="cond_model">
+ − 37 <expand macro="options_ras_to_bounds_model"/>
+ − 38 <when value="Custom">
+ − 39 <param name="model" argument="--model" type="data" format="json, xml" label="Custom model" />
+ − 40 </when>
+ − 41 </conditional>
+ − 42
+ − 43 <conditional name="cond_ras">
+ − 44 <param name="ras_choice" argument="--ras_choice" type="select" label="Do want to use RAS?">
+ − 45 <option value="True" selected="true">Yes</option>
+ − 46 <option value="False">No</option>
+ − 47 </param>
+ − 48 <when value="True">
+ − 49 <param name="input_ras" argument="--input_ras" multiple="false" type="data" format="tabular, csv, tsv" label="RAS matrix:" />
+ − 50 </when>
+ − 51 </conditional>
+ − 52
+ − 53 <conditional name="cond_medium">
+ − 54 <expand macro="options_ras_to_bounds_medium"/>
+ − 55 <when value="Custom">
+ − 56 <param name="medium" argument="--medium" type="data" format="tabular, csv, tsv" label="Custom medium" />
+ − 57 </when>
+ − 58 </conditional>
+ − 59
+ − 60 </inputs>
+ − 61
+ − 62 <outputs>
+ − 63 <data format="txt" name="log" label="RAStoBounds- Log" />
+ − 64
+ − 65 <collection name="ras_to_bounds" type="list" label="Ras to Bounds">
+ − 66 <discover_datasets name = "collection" pattern="__name_and_ext__" directory="ras_to_bounds"/>
+ − 67 </collection>
+ − 68
+ − 69 </outputs>
+ − 70
+ − 71 <help>
+ − 72
+ − 73 <![CDATA[
+ − 74
+ − 75 What it does
+ − 76 -------------
+ − 77
+ − 78 This tool generates the reactions bounds for a given metabolic model (JSON or XML format) with and without the injection of the Reaction Activity Scores (RAS) within the metabolic model.
+ − 79 Moreover, it enables to use custom/pre-defined growth mediums to constrain exchange reactions. For 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 file of bounds is generated for each cell. Otherwise, a single bounds file is returned.
+ − 81
+ − 82 Accepted files:
+ − 83 - 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.
+ − 85 - Medium: tab-separated file containing lower and upper-bounds of medium reactions.
+ − 86
+ − 87 Example medium file
+ − 88 -------------
+ − 89
+ − 90 Custom medium:
+ − 91
+ − 92 +------------+----------------+----------------+
+ − 93 | Reaction ID| lower_bound | upper_bound |
+ − 94 +============+================+================+
+ − 95 | r1 | 0.123167 | 0.371355 |
+ − 96 +------------+----------------+----------------+
+ − 97 | r2 | 0.268765 | 0.765567 |
+ − 98 +------------+----------------+----------------+
+ − 99
+ − 100
+ − 101 Output:
+ − 102 -------------
+ − 103
+ − 104 The tool generates:
+ − 105 - bounds: reporting the bounds of the model, or cells if RAS is used. Format: tab-separated.
+ − 106 - a log file (.txt).
+ − 107 ]]>
+ − 108 </help>
+ − 109 <expand macro="citations" />
+ − 110 </tool>
