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1 <tool id="fluxSampling" name="COBRAxy Model sampling" 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="0.29.0">cobra</requirement>
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9 <requirement type="package" version="4.9.3">lxml</requirement>
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10 </requirements>
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11
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12 <command detect_errors="exit_code">
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13 <![CDATA[
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14 python $__tool_directory__/flux_sampling.py
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15 --input $input
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16 --name $input.element_identifier
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17 #if $algorithm_param.algorithm == 'OPTGP':
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18 --thinning $thinning
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19 --n_batches $n_batches
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20 --n_samples $n_samples
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21 --seed $seed
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22 --output_format $output_format
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23 --out_log $log
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24 ]]>
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25 </command>
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26 <inputs>
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27 <param name="input" argument="--input" type="data" format="xml, json" label="Model:" />
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28
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29 <conditional name="algorithm_param">
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30 <param name="algorithm" argument="--algorithm" type="select" label="Choose sampling algorithm:">
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31 <option value="CBS" selected="true">CBS</option>
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32 <option value="OPTGP">OPTGP</option>
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33 </param>
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34 <when value="OPTGP">
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35 <param name="thinning" argument="--thinning" type="integer" label="Thinning:" />
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36 </when>
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37
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38 </conditional>
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39
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40 <param name="n_batches" argument="--n_batches" type="integer" label="Batches:" default="1"/>
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41
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42 <param name="n_samples" argument="--n_samples" type="integer" label="Samples:" default="1000"/>
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43
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44 <param name="seed" argument="--seed" type="integer" label="Seed:" default="0"/>
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45
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46 <param name="output_format" argument="--output_format" type="select" label="Output files format:">
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47 <option value="p" selected="true">pickle extension (binary, non-editable, pre-parsed)</option>
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48 <option value="csv">Comma Separated Values (csv text file, editable, raw)</option>
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49 </param>
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50 </inputs>
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51
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52 <outputs>
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53 <data format="txt" name="log" label="fluxSampling - $name - Log" />
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54
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55 <collection name="results" type="list" label="Model sampling result ($output_format)">
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56 <discover_datasets name = "collection" pattern="__name_and_ext__" directory="result"/>
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57 </collection>
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58 </outputs>
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59
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60 <help>
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61 <![CDATA[
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62 What it does
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63 -------------
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64
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65 This tool generates feasible samples starting from a model in JSON or XML format by using CBS (Corner-based sampling) and OPTGP (mproved Artificial Centering Hit-and-Run sampler) sampling algorithms.
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66
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67 Accepted files:
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68 - A model: JSON or XML file reporting reactions and rules contained in the model.
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69
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70
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71 Output:
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72 -------------
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73
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74 The tool generates:
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75 - Samples: reporting the sampled fluxes for each reaction in the custom model given. Format: csv or pickle.
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76 - a log file (.txt).
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77 ]]>
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78 </help>
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79 <expand macro="citations" />
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80 </tool> |
