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