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1 <tool id="CustomDataGenerator" name="Custom Data Generator" 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 </requirements>
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13
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14 <command detect_errors="exit_code">
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15 <![CDATA[
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16 python $__tool_directory__/custom_data_generator.py
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17 --input $input
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18 --name $input.element_identifier
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19 --out_log $log
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24
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20 --out_rules $rules
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21 --out_reactions $reactions
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22 --out_bounds $bounds
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23 --out_medium $medium
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4
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24 ]]>
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25 </command>
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26 <inputs>
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27 <param name="input" argument="--input" type="data" format="xml, json" label="Custom model:" />
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28 <param name="name" argument="--name" type="text" label="Model's name:" value="Model" help="Default: Model" />
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29 </inputs>
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30
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31 <outputs>
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24
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32 <data format="txt" name="log" label="${tool.name} - Log" />
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30
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33 <data format="tabular" name="rules" label="rules" />
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34 <data format="tabular" name="reactions" label="reactions" />
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35 <data format="tabular" name="bounds" label="bounds" />
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36 <data format="tabular" name="medium" label="medium" />
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4
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37 </outputs>
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38
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39 <help>
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40 <![CDATA[
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41 What it does
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42 -------------
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43
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44 This tool generates four files containing reactions, rules, reaction bounds and medium composition respectively, starting from a custom model in JSON or XML format.
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45 Reactions and rules can be used as inputs for the RAS and RPS generator tools.
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4
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46
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47 Accepted files:
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48 - A model: JSON or XML file reporting reactions and rules contained in the model.
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49
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50
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51 Output:
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52 -------------
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53
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54 The tool generates:
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27
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55 - rules: reporting the rules for each reaction in the custom model given. Format: csv (tab separated).
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56 - reactions: reporting the reactions in the custom model given. Format: csv (tab separated).
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57 - reaction bounds: reporting the lower and upper bounds of each model reaction. Format: csv (tab separated).
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58 - medium composition: reporting the list of exchange/transport reactions. Format: csv (tab separated).
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4
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59 - a log file (.txt).
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60 ]]>
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61 </help>
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62 <expand macro="citations" />
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63 </tool> |
