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annotate rp2paths.xml @ 2:2452952f7bc2 draft

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author tduigou
date Mon, 03 Apr 2023 08:15:46 +0000
parents e3db7fb2c85e
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1 <tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09" licence="@LICENSE@">
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2 <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.5.0</token>
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5 <token name="@LICENSE@">MIT</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement>
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9 </requirements>
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10 <stdio>
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11 <regex match="TIMEOUT:" level="fatal" />
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12 <regex match="ERROR:" level="fatal" />
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13 <regex match="WARNING:" level="warning" />
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14 </stdio>
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15 <command detect_errors="exit_code"><![CDATA[
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16 mkdir out &&
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17 python -m rp2paths all
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18 '$rp2_pathways'
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19 --outdir out
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20 --timeout '$adv.timeout' &&
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21 cp out/compounds.txt '$compounds' &&
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22 if test -f 'out/out_paths.csv'; then
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23 cp out/out_paths.csv '$master_pathways';
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24 fi
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25 ]]></command>
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26 <inputs>
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27 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways" help="Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis."/>
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28 <section name="adv" title="Advanced Options" expanded="false">
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29 <param name="timeout" type="integer" value="1800" label="Time Out" help="Time out before killing a process (in seconds), default: 30 minutes." />
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30 </section>
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31 </inputs>
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32 <outputs>
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33 <data name="master_pathways" format="csv" label="${tool.name} on ${rp2_pathways.name} : Enumerated Pathways" />
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34 <data name="compounds" format="tabular" label="${tool.name} on ${rp2_pathways.name} : Compounds" />
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35 </outputs>
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36 <tests>
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37 <test>
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38 <!-- test 1: check if identical outputs are produced with default parameters -->
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39 <param name="rp2_pathways" value="retropath2_pathways.csv" />
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40 <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff"/>
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41 <output name="compounds" file="rp2paths_compounds.tsv" ftype="tabular" compare="diff"/>
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42 </test>
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43 </tests>
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44 <help><![CDATA[
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45 RP2paths
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46 ========
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47
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48
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49 **RP2paths** extracts the set of heterologous pathways that lies in a metabolic space file outputted by the `RetroPath2.0 workflow <https://www.myexperiment.org/workflows/4987.html>`_ into individual pathways and enumerate them. This analysis is required to ensure that only pathways fulfilling all the precursor needs are retained for further analysis. This tool takes as input a retrosynthesis network in the CSV file produced by `RetroPath2.0 <https://toolshed.g2.bx.psu.edu/view/tduigou/retropath2/9c8ac9980bd6>`_ , and outputs the enumerated pathways (using `EC numbers <https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/enzyme-commission-number>`_ ) as well as the structure of involved chemicals (as SMILES: Simplified Molecular-Input Line-Entry System) in TSV format.
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50
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52 An example of **enumerated pathways** is illustred in the figure below for the production of a target molecule: `Styrene <https://www.sciencedirect.com/topics/chemical-engineering/styrene>`_. **Compounds** are represented by their structures, and **reactions** by their `EC numbers <https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/enzyme-commission-number>`_.
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53
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54
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55 .. image:: ${static_path}/images/enumerated_pathways.png
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56 :width: 40 %
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57 :align: center
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58
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59 |
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60
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61 Input
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62 -----
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63
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64 Required information:
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65
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66 * **RetroPath2.0 Pathways**\ : Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis.
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67
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68 Advanced options:
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69
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70 * **Time Out**\ : (integer) Timeout before killing a process (in seconds), default: 30 minutes.
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71
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72 Output
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73 ------
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74
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75 * **Enumerated Pathways**\ : Describes all the indiviudal enumerated pathways that produce the compound of interest.
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76 * **Compounds**\ : Describes the structure of all the chemical species involved in all pathways as SMILES (Simplified Molecular-Input Line-Entry System).
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77 ]]></help>
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78 <creator>
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79 <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
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80 </creator>
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81 <citations>
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82 <citation type="doi">10.1016/j.ymben.2017.12.002</citation>
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83 </citations>
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84 </tool>