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annotate selenzy_wrapper.xml @ 2:164ccfcd18ec draft

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planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
author tduigou
date Mon, 01 May 2023 01:34:12 +0000
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2
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
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1 <tool id="selenzy-wrapper" name="Selenzyme" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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2 <description>Performs enzyme selection from a reaction query</description>
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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3 <macros>
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4 <token name="@VERSION_SUFFIX@">0</token>
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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5 <token name="@TOOL_VERSION@">0.3.0</token>
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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6 </macros>
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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7 <requirements>
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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8 <requirement type="package" version="@TOOL_VERSION@">selenzy_wrapper</requirement>
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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9 </requirements>
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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10 <command detect_errors="exit_code"><![CDATA[
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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11 python -m selenzy_wrapper '$pathway' '$uniprot_ids'
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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12 --nb_targets '$adv.nb_targets'
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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13 --d '$adv.direction'
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14 $adv.NoMSA
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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15 --host_taxID '$adv.host_taxID'
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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16 #if str($adv.enzyme_taxIDs) != "":
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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17 --enzyme_taxIDs '$adv.enzyme_taxIDs'
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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18 #end if
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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19 --nb_ids '$adv.nb_ids'
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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20 --to_csv '$uniprot_ids_csv'
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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21 --data-path "\${TMPDIR:-.}"
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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22 ]]></command>
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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23 <inputs>
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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24 <param name="pathway" type="data" format="sbml" label="Pathway (SBML)" />
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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25 <section name="adv" title="Advanced Options" expanded="false">
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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26 <param name="host_taxID" type="integer" value="83333" label="Host taxon ID" help="Taxon ID of the chassis (default: 83333 [E. coli K12])" />
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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27 <param name="enzyme_taxIDs" type="text" value="" label="Comma separated taxon IDs of output enzyme sequences" />
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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28 <param name="nb_ids" type="integer" value="-1" label="Number of uniprot IDs with top score to keep" help=" Number of enzyme IDs to display in results (after taxon IDs filtering) [default = -1 (no limit)]" />
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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29 <param name="nb_targets" type="integer" value="500" min="1" label="Number of targets to display in results" help="Number of targets to display in results (before taxon IDs filtering) [default = 500]" />
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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30 <param name="direction" type="float" value="0" label="Use similarity values for preferred reaction direction only" help="You can choose to rank similarities in both reaction directions or to use only the direction of the reaction based on a consensus list that has been generated according to reaction information based on curated information from MetaCyc (Metabolic Pathway Database) [default=0 (OFF)]" />
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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31 <param argument="--NoMSA" type="boolean" falsevalue="--NoMSA" truevalue="" checked="true" display="checkboxes" label="Do not compute MSA/conservation scores ?" help="Do not compute Multiple Sequence Alignment and conservation scores ? (MSA scores are computed by default)" />
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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32 </section>
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33 </inputs>
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34 <outputs>
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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35 <data name="uniprot_ids" format="sbml" label="Uniprot IDs (SBML)" />
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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36 <data name="uniprot_ids_csv" format="csv" label="Uniprot IDs (CSV)" />
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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37 </outputs>
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38 <tests>
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39 <test>
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40 <!-- test 1: check if identical outputs are produced with default parameters -->
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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41 <param name="pathway" value="pathway.xml" />
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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42 <output name="uniprot_ids" file="uniprod_ids_out.xml" compare="diff" sort="true"/>
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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43 <output name="uniprot_ids_csv" file="uniprod_ids_out.csv" ftype="csv" compare="diff"/>
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44 </test>
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45 </tests>
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46 <help><![CDATA[
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47 Selenzyme
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48 ================
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50 Selenzyme searches for enzymes corresponding to each reaction of the pathway. It performs a reaction similarity search in the reference reaction database `MetaNetX <https://www.metanetx.org/>`_ and outputs an updated SBML file annotated with the enzyme UniProt IDs, as well as in CSV format.
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51
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52 Input
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53 -----
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54
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55 * **Pathway (SBML)**\ : SBML pathway file
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56 * **Number of targets to display in results**\ : (integer) Number of targets to display in results (before taxon IDs filtering) [default = 500]
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57 * **Number of uniprot IDs with top score to keep**\ : (integer) Number of enzyme IDs to display in results (after taxon IDs filtering) [default = -1 (no limit)]
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58 * **Use similarity values for preferred reaction direction only**\ : (float) Use similarity values for preferred reaction direction only [default=0 (OFF)]
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59 * **Do not compute MSA/conservation scores ?**\ : (boolean) Do not compute Multiple Sequence Alignment and conservation scores ? (MSA scores are computed by default)
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60 * **Host taxon ID**\ : (string) Taxon ID of the chassis (default: 83333 [E. coli K12])
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61 * **Comma separated taxon IDs of output enzyme sequences**\ : (string) Comma separated taxon IDs of output enzyme sequences
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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 * **Uniprot IDs (SBML)**\ : Annotated SBML pathway.
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67 * **Uniprot IDs (CSV)**\ : Annotated CSV pathway.
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68
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69 Project Links
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70 ------------------
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71
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72 * `GitHub <https://github.com/brsynth/selenzy-wrapper>`_
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73
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74 Version
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75 ----------
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77 0.3.0
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78
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79 Authors
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80 -------
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81 * **Joan Hérisson**
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82
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83 License
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84 -------
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85
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86 * `MIT <https://github.com/brsynth/selenzy-wrapper/blob/master/LICENSE>`_
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87
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88 Acknowledgments
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89 ---------------
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90
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91 * Thomas Duigou
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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92
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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93 ]]></help>
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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94 <citations>
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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95 <citation type="doi">10.1093/bioinformatics/bty065</citation>
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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96 </citations>
164ccfcd18ec planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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97 </tool>