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annotate selenzy.xml @ 0:481f7c35323d draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Wed, 15 Dec 2021 13:59:04 +0000
parents
children 34a9d136a5bf
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1 <tool id="selenzy-wrapper" name="Selenzyme" version="0.1.0">
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2 <description>Performs enzyme selection from a reaction query</description>
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3 <requirements>
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4 <requirement type="package" version="0.1.0">selenzy_wrapper</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 python -m selenzy_wrapper '$pathway' '$uniprot_ids'
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8 --nb_targets '$adv.nb_targets'
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9 --d '$adv.direction'
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10 #if str($adv.NoMSA) == "false":
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11 --NoMSA
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12 #end if
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13 --taxonIDs '$adv.taxonIDs'
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14 --nb_ids '$adv.nb_ids'
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15 --to_csv '$uniprot_ids_csv'
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16 ]]></command>
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17 <inputs>
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18 <param name="pathway" type="data" format="xml" label="Pathway (SBML)" />
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19 <section name="adv" title="Advanced Options" expanded="false">
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20 <param name="nb_ids" type="integer" value="-1" label="Number of uniprot IDs with top score to keep" />
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21 <param name="nb_targets" type="integer" value="500" label="Number of targets to display in results" />
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22 <param name="direction" type="float" value="0" label="Use similiarity values for preferred reaction direction only" />
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23 <param name="NoMSA" type="boolean" label="Do not compute MSA/conservation scores ?" checked="true" display="checkboxes" />
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24 <param name="taxonIDs" type="text" label="Comma separated taxon ids (first considered as the host)" value="83333" />
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25 </section>
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26 </inputs>
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27 <outputs>
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28 <data name="uniprot_ids" format="xml" label="Uniprot IDs" />
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29 <data name="uniprot_ids_csv" format="csv" label="Uniprot IDs" />
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30 </outputs>
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31 <tests>
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32 <test>
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33 <!-- test 1: check if identical outputs are produced with default parameters -->
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34 <param name="pathway" value="pathway.xml" />
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35 <output name="uniprot_ids" file="uniprod_ids_out.xml" ftype="xml" compare="diff" sort="true"/>
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36 <output name="uniprot_ids_csv" file="uniprod_ids_out.csv" ftype="csv" compare="diff"/>
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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40 Selenzyme
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41 ================
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42
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43 Performs enzyme selection from a reaction query.
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44
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45 Input
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46 -----
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47
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48 * **pathway_file**\ : (string) path to pathway file
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49 * **nb_targets**\ : (integer) Number of targets to display in results (before taxon IDs filtering) [default = 20]
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50 * **nb_ids**\ : (integer) Number of enzyme IDs to display in results (after taxon IDs filtering) [default = -1 (no limit)]
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51 * **direction**\ : (float) Use similiarity values for preferred reaction direction only [default=0 (OFF)]
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52 * **NoMSA**\ : (boolean) Do not compute MSA/conservation scores
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53 * **taxonIDs**\ : (string) Comma separated taxon ids [default: 83333 (E. coli K12)]. The first taxon ID is the one of the chassis, following ones are taxon IDs of output enzyme sequences
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54
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55 Output
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56 ------
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57
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58 * **outfile**\ : (string) Path to output file
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59
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60 Project Links
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61 ------------------
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62
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63 * `GitHub <https://github.com/brsynth/selenzy-wrapper>`_
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64
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65 Version
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66 ----------
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67
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68 0.1.0
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69
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70 Authors
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71 -------
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72 * **Joan Hérisson**
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73
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74 License
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75 -------
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76
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77 * `MIT <https://github.com/brsynth/selenzy-wrapper/blob/master/LICENSE>`_
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78
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79 Acknowledgments
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80 ---------------
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81
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82 * Thomas Duigou
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83
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84 ]]></help>
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85 <citations>
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86 <citation type="bibtex">
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87 @article{10.1093/bioinformatics/bty065,
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88 title={Selenzyme: enzyme selection tool for pathway design},
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89 author={Pablo Carbonell, Jerry Wong, Neil Swainston, Eriko Takano, Nicholas J Turner, Nigel S Scrutton, Douglas B Kell, Rainer Breitling, Jean-Loup Faulon},
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90 volume={34},
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91 pages={2153–2154},
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92 year={2018},
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93 doi = {10.1093/bioinformatics/bty065},
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94 url = {https://doi.org/10.1093/bioinformatics/bty065},
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95 }
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96 </citation>
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97 </citations>
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98 </tool>