Mercurial > repos > bimib > marea_2_0
comparison rps_generator.xml @ 282:d385c4df70c3 draft
Uploaded
| author | luca_milaz |
|---|---|
| date | Mon, 08 Jul 2024 22:16:45 +0000 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 281:65eb6c9c5e8f | 282:d385c4df70c3 |
|---|---|
| 1 <tool id="MaREA RPS Generator" name="Expression2RPS" version="1.0.0"> | |
| 2 <description>- Reaction Propensity Scores computation</description> | |
| 3 <macros> | |
| 4 <import>marea_macros.xml</import> | |
| 5 </macros> | |
| 6 <requirements> | |
| 7 <!--<requirement type="package" version="1.18.5">numpy</requirement> | |
| 8 <requirement type="package" version="1.4.4">pandas</requirement>--> | |
| 9 <requirement type="package" version="4.6.3">lxml</requirement> | |
| 10 </requirements> | |
| 11 <command detect_errors="exit_code"> | |
| 12 <![CDATA[ | |
| 13 python $__tool_directory__/rps_generator.py | |
| 14 --input $input | |
| 15 --reaction_choice $cond_reactions.reaction_choice | |
| 16 --tool_dir $__tool_directory__ | |
| 17 --out_log $log | |
| 18 --rps_output $rps_output | |
| 19 #if $cond_reactions.reaction_choice == 'custom' | |
| 20 --custom $cond_reactions.Custom_react | |
| 21 #end if | |
| 22 ]]> | |
| 23 </command> | |
| 24 <inputs> | |
| 25 <param name="input" argument="--input" type="data" format="tabular, tsv, csv" label="Abundance dataset:" /> | |
| 26 <param name="name" argument="--name" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" /> | |
| 27 | |
| 28 <conditional name="cond_reactions"> | |
| 29 <param name="reaction_choice" argument="--reaction_choice" type="select" label="Choose reaction dataset:"> | |
| 30 <option value="default" selected="true">ENGRO2 reaction dataset </option> | |
| 31 <option value="custom">Custom reaction dataset</option> | |
| 32 </param> | |
| 33 <when value="custom"> | |
| 34 <param name="Custom_react" type="data" format="csv" label="Custom reactions" /> | |
| 35 </when> | |
| 36 </conditional> | |
| 37 </inputs> | |
| 38 | |
| 39 <outputs> | |
| 40 <data format="txt" name="log" label="Expression2RPS - $name - Log" /> | |
| 41 <data format="tabular" name="rps_output" label="$name RPS"/> | |
| 42 </outputs> | |
| 43 | |
| 44 <help> | |
| 45 <![CDATA[ | |
| 46 | |
| 47 What it does | |
| 48 ------------- | |
| 49 | |
| 50 This tool computes Reaction Propensity Scores based on the availability of reaction substrates, for (ideally) each input model reaction and for each sample. | |
| 51 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. | |
| 52 This assumption holds as long as the substrate is in significant excess over the enzyme constant KM. | |
| 53 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. | |
| 54 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. | |
| 55 | |
| 56 Accepted files: | |
| 57 - An abundance dataset: Tab-separated text file reporting the abundance value of each metabolite for each cell line in the dataset. | |
| 58 Column header: cell line ID. | |
| 59 Row header: metabolite ID. | |
| 60 | |
| 61 | |
| 62 Optional files: | |
| 63 - Custom reaction dataset: .csv file specifying for each reaction ID the corresponding formula. | |
| 64 First column: reaction ID | |
| 65 Second column: reaction formula. | |
| 66 | |
| 67 | |
| 68 Output: | |
| 69 ------------- | |
| 70 | |
| 71 The tool generates: | |
| 72 - a tab-separated file(.csv): reporting the RPS values for each reaction and each cell line in the dataset. | |
| 73 - a log file (.txt). | |
| 74 ]]> | |
| 75 </help> | |
| 76 <expand macro="citations" /> | |
| 77 </tool> | |
| 78 |