Mercurial > repos > iuc > rp2paths

annotate rp2paths.xml @ 3:bc7e0b9e8707 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths commit de11e4b7851bf4efeafaf6d8369b75ad22607604
author iuc
date Mon, 17 Nov 2025 12:19:39 +0000
parents a5fb27520253
children
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1 <tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09">
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2 <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description>
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3 <macros>
3
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4 <token name="@TOOL_VERSION@">2.1.4</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement>
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8 </requirements>
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9 <stdio>
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10 <regex match="TIMEOUT:" level="fatal" />
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11 <regex match="ERROR:" level="fatal" />
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12 <regex match="WARNING:" level="warning" />
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13 </stdio>
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14 <command detect_errors="exit_code"><![CDATA[
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15 mkdir out &&
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16 python -m rp2paths all
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17 '$rp2_pathways'
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18 --outdir out
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19 --timeout '$adv.timeout' &&
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20 cp out/compounds.txt '$compounds' &&
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21 if test -f 'out/out_paths.csv'; then
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22 cp out/out_paths.csv '$master_pathways';
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23 fi
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24 ]]></command>
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25 <inputs>
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26 <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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27 <section name="adv" title="Advanced Options" expanded="false">
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28 <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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29 </section>
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30 </inputs>
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31 <outputs>
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32 <data name="master_pathways" format="csv" label="${tool.name} on ${rp2_pathways.name} : Enumerated Pathways" />
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33 <data name="compounds" format="tabular" label="${tool.name} on ${rp2_pathways.name} : Compounds" />
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34 </outputs>
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35 <tests>
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36 <test>
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37 <!-- test 1: check if identical outputs are produced with default parameters -->
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38 <param name="rp2_pathways" value="retropath2_pathways.csv" />
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39 <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff"/>
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40 <output name="compounds" file="rp2paths_compounds.tsv" ftype="tabular" compare="diff"/>
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41 </test>
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42 </tests>
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43 <help><![CDATA[
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44 RP2paths
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45 ========
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46
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47
1
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48 **RP2paths** extracts the set of heterologous pathways that lies in a metabolic space file outputted by the "RetroPath2.0 workflow" into individual pathways and enumerate them.
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49 This analysis is required to ensure that only pathways fulfilling all the precursor needs are retained for further analysis.
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50 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>`_ ,
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51 and outputs the enumerated pathways (using `EC numbers <https://en.wikipedia.org/wiki/Enzyme_Commission_number>`_ ) as well as the structure of involved chemicals (as SMILES: Simplified Molecular-Input Line-Entry System) in TSV format.
0
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54 An example of **enumerated pathways** is illustred in the figure below for the production of a target molecule: `Styrene <https://en.wikipedia.org/wiki/Styrene>`_. **Compounds** are represented by their structures, and **reactions** by their `EC numbers <https://en.wikipedia.org/wiki/Enzyme_Commission_number>`_.
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57 .. image:: ${static_path}/images/enumerated_pathways.png
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58 :width: 40 %
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59 :align: center
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61 |
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63 Input
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64 -----
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66 Required information:
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68 * **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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70 Advanced options:
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72 * **Time Out**\ : (integer) Timeout before killing a process (in seconds), default: 30 minutes.
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74 Output
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75 ------
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77 * **Enumerated Pathways**\ : Describes all the indiviudal enumerated pathways that produce the compound of interest.
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78 * **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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80 Project Links
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81 ---------------------
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83 * `GitHub <https://github.com/brsynth/rp2paths>`_
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84
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85 License
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86 -------
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87
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88 `MIT <https://github.com/brsynth/rp2paths/blob/master/LICENSE.md>`_
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90 Acknowledgments
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91 ---------------
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93 * Joan Hérisson
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95 ]]></help>
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96 <citations>
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97 <citation type="doi">10.1016/j.ymben.2017.12.002</citation>
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98 </citations>
1
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99 </tool>