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comparison rp2paths.xml @ 0:1e7007e80a4b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
author iuc
date Mon, 17 Oct 2022 21:20:40 +0000
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1 <tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09">
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 </macros>
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement>
8 </requirements>
9 <stdio>
10 <regex match="TIMEOUT:" level="fatal" />
11 <regex match="ERROR:" level="fatal" />
12 <regex match="WARNING:" level="warning" />
13 </stdio>
14 <command detect_errors="exit_code"><![CDATA[
15 mkdir out &&
16 python -m rp2paths all
17 '$rp2_pathways'
18 --outdir out
19 --timeout '$adv.timeout' &&
20 cp out/compounds.txt '$compounds' &&
21 if test -f 'out/out_paths.csv'; then
22 cp out/out_paths.csv '$master_pathways';
23 fi
24 ]]></command>
25 <inputs>
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."/>
27 <section name="adv" title="Advanced Options" expanded="false">
28 <param name="timeout" type="integer" value="1800" label="Time Out" help="Time out before killing a process (in seconds), default: 30 minutes." />
29 </section>
30 </inputs>
31 <outputs>
32 <data name="master_pathways" format="csv" label="${tool.name} on ${rp2_pathways.name} : Enumerated Pathways" />
33 <data name="compounds" format="tabular" label="${tool.name} on ${rp2_pathways.name} : Compounds" />
34 </outputs>
35 <tests>
36 <test>
37 <!-- test 1: check if identical outputs are produced with default parameters -->
38 <param name="rp2_pathways" value="retropath2_pathways.csv" />
39 <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff"/>
40 <output name="compounds" file="rp2paths_compounds.tsv" ftype="tabular" compare="diff"/>
41 </test>
42 </tests>
43 <help><![CDATA[
44 RP2paths
45 ========
46
47
48 **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://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.
49
50
51 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>`_.
52
53
54 .. image:: ${static_path}/images/enumerated_pathways.png
55 :width: 40 %
56 :align: center
57
58 |
59
60 Input
61 -----
62
63 Required information:
64
65 * **RetroPath2.0 Pathways**\ : Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis.
66
67 Advanced options:
68
69 * **Time Out**\ : (integer) Timeout before killing a process (in seconds), default: 30 minutes.
70
71 Output
72 ------
73
74 * **Enumerated Pathways**\ : Describes all the indiviudal enumerated pathways that produce the compound of interest.
75 * **Compounds**\ : Describes the structure of all the chemical species involved in all pathways as SMILES (Simplified Molecular-Input Line-Entry System).
76
77 Project Links
78 ---------------------
79
80 * `GitHub <https://github.com/brsynth/rp2paths>`_
81
82 License
83 -------
84
85 `MIT <https://github.com/brsynth/rp2paths/blob/master/LICENSE.md>`_
86
87 Acknowledgments
88 ---------------
89
90 * Joan Hérisson
91
92 ]]></help>
93 <citations>
94 <citation type="doi">10.1016/j.ymben.2017.12.002</citation>
95 </citations>
96 </tool>