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1 <tool id="MaREA RPS Generator" name="Expression2RPS" version="2.0.0">
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2 <description>- Reaction Propensity Scores computation</description>
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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 <requirements>
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7 <requirement type="package" version="1.24.4">numpy</requirement>
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8 <requirement type="package" version="2.0.3">pandas</requirement>
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9 <requirement type="package" version="5.2.2">lxml</requirement>
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10 <requirement type="package" version="0.29.0">cobra</requirement>
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11 </requirements>
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12 <command detect_errors="exit_code">
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13 <![CDATA[
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14 python $__tool_directory__/rps_generator.py
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15 --input $input
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16 --reaction_choice $cond_reactions.reaction_choice
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17 --tool_dir $__tool_directory__
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18 --out_log $log
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19 --rps_output $rps_output
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20 #if $cond_reactions.reaction_choice == 'custom'
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21 --custom $cond_reactions.Custom_react
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22 #end if
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23 ]]>
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24 </command>
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25 <inputs>
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26 <param name="input" argument="--input" type="data" format="tabular, tsv, csv" label="Abundance dataset:" />
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27 <param name="name" argument="--name" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
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28
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29 <conditional name="cond_reactions">
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30 <param name="reaction_choice" argument="--reaction_choice" type="select" label="Choose reaction dataset:">
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31 <option value="default" selected="true">ENGRO2 reaction dataset </option>
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32 <option value="custom">Custom reaction dataset</option>
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33 </param>
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34 <when value="custom">
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35 <param name="Custom_react" type="data" format="csv" label="Custom reactions" />
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36 </when>
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37 </conditional>
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38 </inputs>
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39
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40 <outputs>
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41 <data format="txt" name="log" label="Expression2RPS - $name - Log" />
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42 <data format="tabular" name="rps_output" label="$name RPS"/>
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43 </outputs>
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44
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45 <help>
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46 <![CDATA[
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47
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48 What it does
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49 -------------
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50
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51 This tool computes Reaction Propensity Scores based on the availability of reaction substrates, for (ideally) each input model reaction and for each sample.
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52 The score is computed as the product of the concentrations of the reacting substances, with each concentration raised to a power equal to its stoichiometric coefficient. According to themass action law, the rate of any chemical reaction is indeed proportional to this product.
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53 This assumption holds as long as the substrate is in significant excess over the enzyme constant KM.
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54 If a metabolite is either missing in the model provided with respect to its reactions or it is present in our "black list", the RPS score is set to NaN.
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55 This "black list" of metabolites contains those substrates that are present in too many reactions to be significant. It is defined in the file black_list.pickle and cannot be modified by the user.
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56
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57 Accepted files:
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58 - An abundance dataset: Tab-separated text file reporting the abundance value of each metabolite for each cell line in the dataset.
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59 Column header: cell line ID.
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60 Row header: metabolite ID.
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61
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62
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63 Optional files:
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64 - Custom reaction dataset: .csv file specifying for each reaction ID the corresponding formula.
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65 First column: reaction ID
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66 Second column: reaction formula.
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67
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68
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69 Output:
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70 -------------
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71
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72 The tool generates:
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73 - a tab-separated file(.csv): reporting the RPS values for each reaction and each cell line in the dataset.
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74 - a log file (.txt).
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75 ]]>
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76 </help>
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77 <expand macro="citations" />
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78 </tool>
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79
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