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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 --output_format $output_format
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20 --out_log $log
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21 ]]>
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22 </command>
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23 <inputs>
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24 <param name="input" argument="--input" type="data" format="xml, json" label="Custom model:" />
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25 <param name="name" argument="--name" type="text" label="Model's name:" value="Model" help="Default: Model" />
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26
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27 <param name="output_format" argument="--output_format" type="select" label="Output files format:">
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28 <option value="p" selected="true">pickle extension (binary, non-editable, pre-parsed)</option>
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29 <option value="csv">Comma Separated Values (csv text file, editable, raw)</option>
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30 </param>
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31 </inputs>
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32
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33 <outputs>
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34 <data format="txt" name="log" label="CustomDataGenerator - $name - Log" />
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35
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36 <collection name="results" type="list" label="Custom Data Results ($output_format)">
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37 <discover_datasets name = "collection" pattern="__name_and_ext__" directory="result"/>
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38 </collection>
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39 </outputs>
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40
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41 <help>
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42 <![CDATA[
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43 What it does
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44 -------------
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45
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46 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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47 Reactions and rules can be used as inputs for the RAS and RPS generator tools.
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4
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48
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49 Accepted files:
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50 - A model: JSON or XML file reporting reactions and rules contained in the model.
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51
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52
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53 Output:
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54 -------------
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55
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56 The tool generates:
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57 - rules: reporting the rules for each reaction in the custom model given. Format: csv or pickle.
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58 - reactions: reporting the reactions in the custom model given. Format: csv or pickle.
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59 - reaction bounds: reporting the lower and upper bounds of each model reaction. Format: csv or pickle.
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60 - medium composition: reporting the list of exchange/transport reactions. Format: csv or pickle.
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4
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61 - a log file (.txt).
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62 ]]>
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63 </help>
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64 <expand macro="citations" />
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65 </tool> |
