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annotate selenzy.xml @ 1:34a9d136a5bf draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Tue, 08 Feb 2022 11:12:28 +0000
parents 481f7c35323d
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1 <tool id="selenzy-wrapper" name="Selenzyme" version="@TOOL_VERSION@" profile="19.09">
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2 <description>Performs enzyme selection from a reaction query</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.2.0</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">selenzy_wrapper</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 python -m selenzy_wrapper '$pathway' '$uniprot_ids'
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11 --nb_targets '$adv.nb_targets'
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12 --d '$adv.direction'
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13 #if str($adv.NoMSA) == "false":
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14 --NoMSA
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15 #end if
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16 --host_taxID '$adv.host_taxID'
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17 #if str($adv.enzyme_taxIDs) != "":
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18 --enzyme_taxIDs '$adv.enzyme_taxIDs'
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19 #end if
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20 --nb_ids '$adv.nb_ids'
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21 --to_csv '$uniprot_ids_csv'
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22 ]]></command>
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23 <inputs>
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24 <param name="pathway" type="data" format="xml" label="Pathway (SBML)" />
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25 <section name="adv" title="Advanced Options" expanded="false">
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26 <param name="host_taxID" type="integer" value="83333" label="Host taxon ID" />
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27 <param name="enzyme_taxIDs" type="text" value="" label="Comma separated taxon IDs of output enzyme sequences" />
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28 <param name="nb_ids" type="integer" value="-1" label="Number of uniprot IDs with top score to keep" />
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29 <param name="nb_targets" type="integer" value="500" label="Number of targets to display in results" />
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30 <param name="direction" type="float" value="0" label="Use similiarity values for preferred reaction direction only" />
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31 <param name="NoMSA" type="boolean" checked="true" display="checkboxes" label="Do not compute MSA/conservation scores ?" />
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32 </section>
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33 </inputs>
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34 <outputs>
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35 <data name="uniprot_ids" format="xml" label="Uniprot IDs" />
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36 <data name="uniprot_ids_csv" format="csv" label="Uniprot IDs" />
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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 -->
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41 <param name="pathway" value="pathway.xml" />
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42 <output name="uniprot_ids" file="uniprod_ids_out.xml" ftype="xml" compare="diff" sort="true"/>
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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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49
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50 Performs enzyme selection from a reaction query.
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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_file**\ : (string) path to pathway file
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56 * **nb_targets**\ : (integer) Number of targets to display in results (before taxon IDs filtering) [default = 20]
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57 * **nb_ids**\ : (integer) Number of enzyme IDs to display in results (after taxon IDs filtering) [default = -1 (no limit)]
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58 * **direction**\ : (float) Use similiarity values for preferred reaction direction only [default=0 (OFF)]
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59 * **NoMSA**\ : (boolean) Do not compute MSA/conservation scores
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60 * **host_taxID**\ : (string) Taxon ID of the chassis (default: 83333 [E. coli K12])
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61 * **enzyme_taxIDs**\ : (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 * **outfile**\ : (string) Path to output file
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67
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68 Project Links
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69 ------------------
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70
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71 * `GitHub <https://github.com/brsynth/selenzy-wrapper>`_
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72
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73 Version
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74 ----------
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75
1
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76 0.2.0
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77
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78 Authors
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79 -------
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80 * **Joan Hérisson**
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81
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82 License
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83 -------
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84
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85 * `MIT <https://github.com/brsynth/selenzy-wrapper/blob/master/LICENSE>`_
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86
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87 Acknowledgments
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88 ---------------
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89
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90 * Thomas Duigou
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91
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92 ]]></help>
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93 <citations>
1
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94 <citation type="doi">10.1093/bioinformatics/bty065</citation>
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95 </citations>
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96 </tool>