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annotate rp2paths.xml @ 1:2c788cd11881 draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Thu, 02 Dec 2021 12:25:16 +0000
parents
children 550f1c02caba
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1 <tool id="rp2paths" name="RP2paths" version="1.4.3">
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2 <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description>
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3 <requirements>
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4 <requirement type="package" version="1.4.3">rp2paths</requirement>
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5 </requirements>
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6 <stdio>
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7 <regex match="TIMEOUT:" level="fatal" />
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8 <regex match="ERROR:" level="fatal" />
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9 <regex match="WARNING:" level="warning" />
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10 </stdio>
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11 <command detect_errors="exit_code"><![CDATA[
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12 #from os import path as os_path
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13 cd /tmp &&
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14 #set outFolder = os_path.basename(str($master_pathways))
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15 mkdir '$outFolder' &&
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16 python -m rp2paths all
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17 '$rp2_pathways'
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18 --outdir '$outFolder'
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19 --timeout '$adv.timeout' &&
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20 cp '$outFolder'/compounds.txt '$compounds' &&
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21 cp '$outFolder'/out_paths.csv '$master_pathways' &&
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22 rm -rf $outFolder
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23 ]]></command>
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24 <inputs>
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25 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways" />
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26 <section name="adv" title="Advanced Options" expanded="false">
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27 <param name="timeout" type="integer" value="1800" label="Time Out" />
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28 </section>
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29 </inputs>
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30 <outputs>
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31 <data name="master_pathways" format="csv" label="${tool.name} (Pathways)" />
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32 <data name="compounds" format="tsv" label="${tool.name} (Compounds)" />
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33 </outputs>
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34 <tests>
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35 <test>
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36 <!-- test 1: check if identical outputs are produced with default parameters -->
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37 <param name="rp2_pathways" value="retropath2_pathways.csv" />
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38 <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff"/>
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39 <output name="compounds" file="rp2paths_compounds.tsv" ftype="tsv" compare="diff"/>
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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43 rp2paths
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44 ========
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45
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46
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47 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>`_.
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48
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49 Input
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50 -----
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51
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52 Required information:
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53
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54
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55 * **rp_results**\ : (string) Path to the ReatroPath2.0 pathways file
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56
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57 Advanced options:
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58
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59
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60 * **timeout**\ : (string, default: 30 minutes) Time out time of the tool
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61 * **server_url**\ : (string) IP address of the rp2paths REST service
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62
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63 Output
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64 ------
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65
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66
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67 * **out_paths**\ : (string) Path to the RP2paths pathways. Describes all the indiviudal enumerated pathways that produce the compound of interest.
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68 * **out_compounds**\ : (string) Path to the RP2paths Compounds. Describes the structure of all the chemical species involved in all pathways.
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69
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70 Versioning
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71 ----------
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72
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73 v1.4.3
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74
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75 Authors
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76 -------
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77
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78
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79 * **Melchior du Lac**
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80 * Thomas Duigou
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81 * Baudoin Delépine
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82 * Pablo Carbonell
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83
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84 License
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85 -------
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86
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87 `MIT <https://github.com/brsynth/rp2paths/blob/master/LICENSE.md>`_
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88
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89 Acknowledgments
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90 ---------------
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91
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92
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93 * Joan Hérisson
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94
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95 ]]></help>
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96 <citations>
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97 <citation type="bibtex">
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98 @article{delepine2018retropath2,
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99 title={RetroPath2.0: a retrosynthesis workflow for metabolic engineers},
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100 author={Del{\'e}pine, Baudoin and Duigou, Thomas and Carbonell, Pablo and Faulon, Jean-Loup},
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101 journal={Metabolic engineering},
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102 volume={45},
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103 pages={158--170},
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104 year={2018},
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105 publisher={Elsevier}}
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106 </citation>
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107 </citations>
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108 </tool>