4
+ − 1 <tool id="MaREA RPS Generator" name="Expression2RPS" version="2.0.0">
+ − 2 <description>- Reaction Propensity Scores computation</description>
+ − 3 <macros>
+ − 4 <import>marea_macros.xml</import>
+ − 5 </macros>
+ − 6 <requirements>
+ − 7 <requirement type="package" version="1.24.4">numpy</requirement>
+ − 8 <requirement type="package" version="2.0.3">pandas</requirement>
+ − 9 <requirement type="package" version="5.2.2">lxml</requirement>
+ − 10 <requirement type="package" version="0.29.0">cobra</requirement>
+ − 11 </requirements>
+ − 12 <command detect_errors="exit_code">
+ − 13 <![CDATA[
+ − 14 python $__tool_directory__/rps_generator.py
+ − 15 --input $input
+ − 16 --reaction_choice $cond_reactions.reaction_choice
+ − 17 --tool_dir $__tool_directory__
+ − 18 --out_log $log
+ − 19 --rps_output $rps_output
+ − 20 #if $cond_reactions.reaction_choice == 'custom'
+ − 21 --custom $cond_reactions.Custom_react
+ − 22 #end if
+ − 23 ]]>
+ − 24 </command>
+ − 25 <inputs>
+ − 26 <param name="input" argument="--input" type="data" format="tabular, tsv, csv" label="Abundance dataset:" />
+ − 27 <param name="name" argument="--name" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
+ − 28
+ − 29 <conditional name="cond_reactions">
+ − 30 <param name="reaction_choice" argument="--reaction_choice" type="select" label="Choose reaction dataset:">
+ − 31 <option value="default" selected="true">ENGRO2 reaction dataset </option>
+ − 32 <option value="custom">Custom reaction dataset</option>
+ − 33 </param>
+ − 34 <when value="custom">
+ − 35 <param name="Custom_react" type="data" format="csv" label="Custom reactions" />
+ − 36 </when>
+ − 37 </conditional>
+ − 38 </inputs>
+ − 39
+ − 40 <outputs>
+ − 41 <data format="txt" name="log" label="Expression2RPS - $name - Log" />
+ − 42 <data format="tabular" name="rps_output" label="$name RPS"/>
+ − 43 </outputs>
+ − 44
+ − 45 <help>
+ − 46 <![CDATA[
+ − 47
+ − 48 What it does
+ − 49 -------------
+ − 50
+ − 51 This tool computes Reaction Propensity Scores based on the availability of reaction substrates, for (ideally) each input model reaction and for each sample.
+ − 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.
+ − 53 This assumption holds as long as the substrate is in significant excess over the enzyme constant KM.
+ − 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.
+ − 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.
+ − 56
+ − 57 Accepted files:
+ − 58 - An abundance dataset: Tab-separated text file reporting the abundance value of each metabolite for each cell line in the dataset.
+ − 59 Column header: cell line ID.
+ − 60 Row header: metabolite ID.
+ − 61
+ − 62
+ − 63 Optional files:
+ − 64 - Custom reaction dataset: .csv file specifying for each reaction ID the corresponding formula.
+ − 65 First column: reaction ID
+ − 66 Second column: reaction formula.
+ − 67
+ − 68
+ − 69 Output:
+ − 70 -------------
+ − 71
+ − 72 The tool generates:
+ − 73 - a tab-separated file(.csv): reporting the RPS values for each reaction and each cell line in the dataset.
+ − 74 - a log file (.txt).
+ − 75 ]]>
+ − 76 </help>
+ − 77 <expand macro="citations" />
+ − 78 </tool>
+ − 79