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+ − 1 <tool id="fluxSimulation" name="Flux Simulation" 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 <requirement type="package" version="1.10.1">scipy</requirement>
+ − 14 </requirements>
+ − 15
+ − 16 <command detect_errors="exit_code">
+ − 17 <![CDATA[
+ − 18 python $__tool_directory__/flux_simulation.py
+ − 19 --tool_dir $__tool_directory__
+ − 20 --model_selector $cond_model.model_selector
+ − 21 #if $cond_model.model_selector == 'Custom'
+ − 22 --model $model
+ − 23 --model_name $model.element_identifier
+ − 24 #end if
+ − 25 --input "${",".join(map(str, $inputs))}"
+ − 26 #set $names = ""
+ − 27 #for $input_temp in $inputs:
+ − 28 #set $names = $names + $input_temp.element_identifier + ","
+ − 29 #end for
+ − 30 --name $names
+ − 31 --thinning 0
+ − 32 #if $algorithm_param.algorithm == 'OPTGP':
+ − 33 --thinning $algorithm_param.thinning
+ − 34 #end if
+ − 35 --algorithm $algorithm_param.algorithm
+ − 36 --n_batches $n_batches
+ − 37 --n_samples $n_samples
+ − 38 --seed $seed
+ − 39 --output_type "${",".join(map(str, $output_types))}"
+ − 40 --output_type_analysis "${",".join(map(str, $output_types_analysis))}"
+ − 41 --out_log $log
+ − 42 ]]>
+ − 43 </command>
+ − 44 <inputs>
+ − 45
+ − 46 <conditional name="cond_model">
+ − 47 <expand macro="options_ras_to_bounds_model"/>
+ − 48 <when value="Custom">
+ − 49 <param name="model" argument="--model" type="data" format="json, xml" label="Custom model" />
+ − 50 </when>
+ − 51 </conditional>
+ − 52
+ − 53 <param name="inputs" argument="--inputs" multiple="true" type="data" format="tabular, csv, tsv" label="Bound(s):" />
+ − 54
+ − 55
+ − 56 <conditional name="algorithm_param">
+ − 57 <param name="algorithm" argument="--algorithm" type="select" label="Choose sampling algorithm:">
+ − 58 <option value="CBS" selected="true">CBS</option>
+ − 59 <option value="OPTGP">OPTGP</option>
+ − 60 </param>
+ − 61 <when value="OPTGP">
+ − 62 <param name="thinning" argument="--thinning" type="integer" label="Thinning:" value="100" help="Number of iterations to wait before taking a sample."/>
+ − 63 </when>
+ − 64
+ − 65 </conditional>
+ − 66
+ − 67
+ − 68 <param name="n_samples" argument="--n_samples" type="integer" label="Samples:" value="1000"/>
+ − 69
229
+ − 70 <param name="n_batches" argument="--n_batches" type="integer" label="Batches:" value="1" help="This is useful for computational perfomances."/>
93
+ − 71
+ − 72 <param name="seed" argument="--seed" type="integer" label="Seed:" value="0" helph="Random seed."/>
+ − 73
+ − 74 <param type="select" argument="--output_types" multiple="true" name="output_types" label="Desired outputs from sampling">
+ − 75 <option value="mean" selected="true">Mean</option>
+ − 76 <option value="median" selected="true">Median</option>
+ − 77 <option value="quantiles" selected="true">Quantiles</option>
+ − 78 <option value="fluxes" selected="false">All fluxes</option>
+ − 79 </param>
+ − 80
+ − 81 <param type="select" argument="--output_types_analysis" multiple="true" name="output_types_analysis" label="Desired outputs from flux analysis">
+ − 82 <option value="pFBA" selected="false">pFBA</option>
+ − 83 <option value="FVA" selected="false">FVA</option>
+ − 84 <option value="sensitivity" selected="false">Sensitivity reaction knock-out (Biomass)</option>
+ − 85 </param>
+ − 86 </inputs>
+ − 87
+ − 88
+ − 89 <outputs>
+ − 90 <data format="txt" name="log" label="Flux Simulation - Log" />
+ − 91
+ − 92 <data name="output" format="tabular" label="Flux Simulation - Output">
+ − 93 <discover_datasets pattern="__name_and_ext__"
+ − 94 directory="flux_simulation" visible="true" />
+ − 95 </data>
+ − 96
+ − 97 </outputs>
+ − 98
+ − 99 <help>
+ − 100 <![CDATA[
+ − 101 What it does
+ − 102 -------------
+ − 103
+ − 104 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.
+ − 105
+ − 106 It can return sampled fluxes by appliying summary statistics:
+ − 107 - mean
+ − 108 - median
+ − 109 - quantiles (0.25, 0.50, 0.75).
+ − 110
+ − 111 Flux analysis can be perfomed over the metabolic model:
+ − 112 - parsimoniuos-FBA (optimized by Biomass)
+ − 113 - FVA
+ − 114 - 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.
+ − 115
+ − 116 Accepted files:
+ − 117 - A model: JSON or XML file reporting reactions and rules contained in the model. It can be ENGRO2 or a custom model.
+ − 118 - Context-specific bounds: generated by RAS to Bounds tool. This can be a collection of bounds too (one bounds file per context).
+ − 119
+ − 120 Output:
+ − 121 -------------
+ − 122
+ − 123 The tool generates:
+ − 124 - Samples: reporting the sampled fluxes for each reaction (reaction names on the rows and sample names on the columns). Format: tab-separated.
+ − 125 - a log file (.txt).
+ − 126
+ − 127 **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.
+ − 128 **TIP**: The Thinning parameter of the OPTGP algorithm is useful to converge to a stationary distribution (see cited articles by Galuzzi, Milazzo and Damiani).
+ − 129
+ − 130 ]]>
+ − 131 </help>
+ − 132 <expand macro="citations_fluxes" />
+ − 133
+ − 134 </tool>