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planemo upload commit 0b2a2717ffa780fabd61d34f676204e8842b5c16
author tduigou
date Mon, 03 Apr 2023 08:15:46 +0000
parents e3db7fb2c85e
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1 <tool id="rp2paths" name="RP2paths" version="1.5.0"> 1 <tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09" licence="@LICENSE@">
2 <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description> 2 <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.5.0</token>
5 <token name="@LICENSE@">MIT</token>
6 </macros>
3 <requirements> 7 <requirements>
4 <requirement type="package" version="1.5.0">rp2paths</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement>
5 </requirements> 9 </requirements>
6 <stdio> 10 <stdio>
7 <regex match="TIMEOUT:" level="fatal" /> 11 <regex match="TIMEOUT:" level="fatal" />
8 <regex match="ERROR:" level="fatal" /> 12 <regex match="ERROR:" level="fatal" />
9 <regex match="WARNING:" level="warning" /> 13 <regex match="WARNING:" level="warning" />
10 </stdio> 14 </stdio>
11 <command detect_errors="exit_code"><![CDATA[ 15 <command detect_errors="exit_code"><![CDATA[
12 mkdir out && 16 mkdir out &&
13 python -m rp2paths all 17 python -m rp2paths all
14 '$rp2_pathways' 18 '$rp2_pathways'
15 --outdir out 19 --outdir out
16 --timeout '$adv.timeout' && 20 --timeout '$adv.timeout' &&
17 if test -f "out/compounds.txt"; then 21 cp out/compounds.txt '$compounds' &&
18 cp out/compounds.txt '$compounds'; 22 if test -f 'out/out_paths.csv'; then
19 cp out/out_paths.csv '$master_pathways'; 23 cp out/out_paths.csv '$master_pathways';
20 fi 24 fi
21 ]]></command> 25 ]]></command>
22 <inputs> 26 <inputs>
23 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways" /> 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."/>
24 <section name="adv" title="Advanced Options" expanded="false"> 28 <section name="adv" title="Advanced Options" expanded="false">
25 <param name="timeout" type="integer" value="1800" label="Time Out" /> 29 <param name="timeout" type="integer" value="1800" label="Time Out" help="Time out before killing a process (in seconds), default: 30 minutes." />
26 </section> 30 </section>
27 </inputs> 31 </inputs>
28 <outputs> 32 <outputs>
29 <data name="master_pathways" format="csv" label="${tool.name} (Pathways)" /> 33 <data name="master_pathways" format="csv" label="${tool.name} on ${rp2_pathways.name} : Enumerated Pathways" />
30 <data name="compounds" format="tsv" label="${tool.name} (Compounds)" /> 34 <data name="compounds" format="tabular" label="${tool.name} on ${rp2_pathways.name} : Compounds" />
31 </outputs> 35 </outputs>
32 <tests> 36 <tests>
33 <test> 37 <test>
34 <!-- test 1: check if identical outputs are produced with default parameters --> 38 <!-- test 1: check if identical outputs are produced with default parameters -->
35 <param name="rp2_pathways" value="retropath2_pathways.csv" /> 39 <param name="rp2_pathways" value="retropath2_pathways.csv" />
36 <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff"/> 40 <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff"/>
37 <output name="compounds" file="rp2paths_compounds.tsv" ftype="tsv" compare="diff"/> 41 <output name="compounds" file="rp2paths_compounds.tsv" ftype="tabular" compare="diff"/>
38 </test> 42 </test>
39 </tests> 43 </tests>
40 <help><![CDATA[ 44 <help><![CDATA[
41 rp2paths 45 RP2paths
42 ======== 46 ========
43 47
44 48
45 RP2paths extracts the set of pathways that lies in a metabolic space file output by the RetroPath2.0 workflow. Source code may be found at the following location: `GitHub <https://github.com/brsynth/rp2paths>`_. 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.
50
51
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>`_.
53
54
55 .. image:: ${static_path}/images/enumerated_pathways.png
56 :width: 40 %
57 :align: center
58
59 |
46 60
47 Input 61 Input
48 ----- 62 -----
49 63
50 Required information: 64 Required information:
51 65
52 66 * **RetroPath2.0 Pathways**\ : Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis.
53 * **rp_results**\ : (string) Path to the ReatroPath2.0 pathways file
54 67
55 Advanced options: 68 Advanced options:
56 69
57 70 * **Time Out**\ : (integer) Timeout before killing a process (in seconds), default: 30 minutes.
58 * **timeout**\ : (string, default: 30 minutes) Time out time of the tool
59 * **server_url**\ : (string) IP address of the rp2paths REST service
60 71
61 Output 72 Output
62 ------ 73 ------
63 74
64 75 * **Enumerated Pathways**\ : Describes all the indiviudal enumerated pathways that produce the compound of interest.
65 * **out_paths**\ : (string) Path to the RP2paths pathways. Describes all the indiviudal enumerated pathways that produce the compound of interest. 76 * **Compounds**\ : Describes the structure of all the chemical species involved in all pathways as SMILES (Simplified Molecular-Input Line-Entry System).
66 * **out_compounds**\ : (string) Path to the RP2paths Compounds. Describes the structure of all the chemical species involved in all pathways.
67
68 Versioning
69 ----------
70
71 v1.4.3
72
73 Authors
74 -------
75
76
77 * **Melchior du Lac**
78 * Thomas Duigou
79 * Baudoin Delépine
80 * Pablo Carbonell
81
82 License
83 -------
84
85 `MIT <https://github.com/brsynth/rp2paths/blob/master/LICENSE.md>`_
86
87 Acknowledgments
88 ---------------
89
90
91 * Joan Hérisson
92
93 ]]></help> 77 ]]></help>
78 <creator>
79 <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
80 </creator>
94 <citations> 81 <citations>
95 <citation type="bibtex"> 82 <citation type="doi">10.1016/j.ymben.2017.12.002</citation>
96 @article{delepine2018retropath2,
97 title={RetroPath2.0: a retrosynthesis workflow for metabolic engineers},
98 author={Del{\'e}pine, Baudoin and Duigou, Thomas and Carbonell, Pablo and Faulon, Jean-Loup},
99 journal={Metabolic engineering},
100 volume={45},
101 pages={158--170},
102 year={2018},
103 publisher={Elsevier}}
104 </citation>
105 </citations> 83 </citations>
106 </tool> 84 </tool>