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1 <tool id="fluxSimulation" name="Flux Simulation" 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 <requirement type="package" version="1.10.1">scipy</requirement>
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14 </requirements>
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15
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16 <command detect_errors="exit_code">
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17 <![CDATA[
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18 python $__tool_directory__/flux_simulation.py
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19 --tool_dir $__tool_directory__
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20 --model_selector $cond_model.model_selector
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21 #if $cond_model.model_selector == 'Custom'
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22 --model $model
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23 --model_name $model.element_identifier
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24 #end if
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25 --input "${",".join(map(str, $inputs))}"
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26 #set $names = ""
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27 #for $input_temp in $inputs:
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28 #set $names = $names + $input_temp.element_identifier + ","
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29 #end for
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30 --name $names
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31 --thinning 0
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32 #if $algorithm_param.algorithm == 'OPTGP':
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33 --thinning $algorithm_param.thinning
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34 #end if
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35 --algorithm $algorithm_param.algorithm
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36 --n_batches $n_batches
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37 --n_samples $n_samples
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38 --seed $seed
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39 --output_type "${",".join(map(str, $output_types))}"
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40 --output_type_analysis "${",".join(map(str, $output_types_analysis))}"
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41 --out_log $log
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42 ]]>
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43 </command>
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44 <inputs>
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45
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46 <conditional name="cond_model">
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47 <expand macro="options_ras_to_bounds_model"/>
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48 <when value="Custom">
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49 <param name="model" argument="--model" type="data" format="json, xml" label="Custom model" />
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50 </when>
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51 </conditional>
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52
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53 <param name="inputs" argument="--inputs" multiple="true" type="data" format="tabular, csv, tsv" label="Bound(s):" />
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54
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55
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56 <conditional name="algorithm_param">
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57 <param name="algorithm" argument="--algorithm" type="select" label="Choose sampling algorithm:">
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58 <option value="CBS" selected="true">CBS</option>
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59 <option value="OPTGP">OPTGP</option>
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60 </param>
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61 <when value="OPTGP">
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62 <param name="thinning" argument="--thinning" type="integer" label="Thinning:" value="100" help="Number of iterations to wait before taking a sample."/>
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63 </when>
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64
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65 </conditional>
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66
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67
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68 <param name="n_samples" argument="--n_samples" type="integer" label="Samples:" value="1000"/>
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69
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70 <param name="n_batches" argument="--n_batches" type="integer" label="Batches:" value="10" help="This is useful for computational perfomances."/>
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71
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72 <param name="seed" argument="--seed" type="integer" label="Seed:" value="0" helph="Random seed."/>
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73
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74 <param type="select" argument="--output_types" multiple="true" name="output_types" label="Desired outputs from sampling">
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75 <option value="mean" selected="true">Mean</option>
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76 <option value="median" selected="true">Median</option>
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77 <option value="quantiles" selected="true">Quantiles</option>
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78 <option value="fluxes" selected="false">All fluxes</option>
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79 </param>
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80
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81 <param type="select" argument="--output_types_analysis" multiple="true" name="output_types_analysis" label="Desired outputs from flux analysis">
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82 <option value="pFBA" selected="false">pFBA</option>
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83 <option value="FVA" selected="false">FVA</option>
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84 <option value="sensitivity" selected="false">Sensitivity reaction knock-out (Biomass)</option>
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85 </param>
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86 </inputs>
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87
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88
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89 <outputs>
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90 <data format="txt" name="log" label="fluxSimulation - Log" />
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91 <collection name="results" type="list" label="${tool.name} - Samples">
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92 <discover_datasets pattern="__name_and_ext__" directory="flux_simulation"/>
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93 </collection>
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94 </outputs>
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95
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96
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97 <help>
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98 <![CDATA[
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99 What it does
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100 -------------
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101
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10
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102 This tool generates flux samples starting from a model in JSON or XML format by using CBS (Corner-based sampling) or OPTGP (Improved Artificial Centering Hit-and-Run sampler) sampling algorithms.
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103
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104 It can return sampled fluxes by appliying summary statistics:
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105 - mean
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106 - median
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107 - quantiles (0.25, 0.50, 0.75).
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108
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109 Flux analysis can be perfomed over the metabolic model:
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110 - parsimoniuos-FBA (optimized by Biomass)
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111 - FVA
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112 - Biomass sensitivity analysis (single reaction knock-out). It is the ratio between the optimal of the Biomass reaction computed by FBA after knocking-out a reaction and the same over the complete model.
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113
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114 Accepted files:
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115 - A model: JSON or XML file reporting reactions and rules contained in the model. It can be ENGRO2 or a custom model.
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116 - Context-specific bounds: generated by RAS to Bounds tool. This can be a collection of bounds too (one bounds file per context).
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117
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118 Output:
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119 -------------
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120
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121 The tool generates:
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122 - Samples: reporting the sampled fluxes for each reaction (reaction names on the rows and sample names on the columns). Format: csv.
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123 - a log file (.txt).
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124
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125 **TIP**: The Batches parameter is useful to mantain in memory just a batch of samples at time. For example, if you wish to sample 10.000 points, than it is suggested to select n_samples = 1.000 and n_batches=10.
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126 **TIP**: The Thinning parameter of the OPTGP algorithm is useful to converge to a stationary distribution (see cited articles by Galuzzi, Milazzo and Damiani).
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127
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128 ]]>
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129 </help>
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130
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12
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131
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132 <citations>
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133 <citation type="bibtex">
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134 @article{galuzzi2024adjusting,
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135 title={Adjusting for false discoveries in constraint-based differential metabolic flux analysis},
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136 author={Galuzzi, Bruno G and Milazzo, Luca and Damiani, Chiara},
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137 journal={Journal of Biomedical Informatics},
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138 volume={150},
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139 pages={104597},
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140 year={2024},
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141 publisher={Elsevier}
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142 }
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143 </citation>
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144 <citation type="bibtex">
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145 @inproceedings{galuzzi2022best,
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146 title={Best practices in flux sampling of constrained-based models},
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147 author={Galuzzi, Bruno G and Milazzo, Luca and Damiani, Chiara},
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148 booktitle={International Conference on Machine Learning, Optimization, and Data Science},
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149 pages={234--248},
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150 year={2022},
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151 organization={Springer}
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152 }
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153 </citation>
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154 <citation type="bibtex">
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155 @article{ebrahim2013cobrapy,
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156 title={COBRApy: constraints-based reconstruction and analysis for python},
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157 author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R},
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158 journal={BMC systems biology},
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159 volume={7},
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160 pages={1--6},
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161 year={2013},
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162 publisher={Springer}
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163 }
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164 </citation>
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165 </citations>
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166
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167 </tool> |
