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comparison 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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1:34a9d136a5bf 2:164ccfcd18ec
1 <tool id="selenzy-wrapper" name="Selenzyme" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <description>Performs enzyme selection from a reaction query</description>
3 <macros>
4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@TOOL_VERSION@">0.3.0</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">selenzy_wrapper</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 python -m selenzy_wrapper '$pathway' '$uniprot_ids'
12 --nb_targets '$adv.nb_targets'
13 --d '$adv.direction'
14 $adv.NoMSA
15 --host_taxID '$adv.host_taxID'
16 #if str($adv.enzyme_taxIDs) != "":
17 --enzyme_taxIDs '$adv.enzyme_taxIDs'
18 #end if
19 --nb_ids '$adv.nb_ids'
20 --to_csv '$uniprot_ids_csv'
21 --data-path "\${TMPDIR:-.}"
22 ]]></command>
23 <inputs>
24 <param name="pathway" type="data" format="sbml" label="Pathway (SBML)" />
25 <section name="adv" title="Advanced Options" expanded="false">
26 <param name="host_taxID" type="integer" value="83333" label="Host taxon ID" help="Taxon ID of the chassis (default: 83333 [E. coli K12])" />
27 <param name="enzyme_taxIDs" type="text" value="" label="Comma separated taxon IDs of output enzyme sequences" />
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)]" />
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]" />
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)]" />
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)" />
32 </section>
33 </inputs>
34 <outputs>
35 <data name="uniprot_ids" format="sbml" label="Uniprot IDs (SBML)" />
36 <data name="uniprot_ids_csv" format="csv" label="Uniprot IDs (CSV)" />
37 </outputs>
38 <tests>
39 <test>
40 <!-- test 1: check if identical outputs are produced with default parameters -->
41 <param name="pathway" value="pathway.xml" />
42 <output name="uniprot_ids" file="uniprod_ids_out.xml" compare="diff" sort="true"/>
43 <output name="uniprot_ids_csv" file="uniprod_ids_out.csv" ftype="csv" compare="diff"/>
44 </test>
45 </tests>
46 <help><![CDATA[
47 Selenzyme
48 ================
49
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.
51
52 Input
53 -----
54
55 * **Pathway (SBML)**\ : SBML pathway file
56 * **Number of targets to display in results**\ : (integer) Number of targets to display in results (before taxon IDs filtering) [default = 500]
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)]
58 * **Use similarity values for preferred reaction direction only**\ : (float) Use similarity values for preferred reaction direction only [default=0 (OFF)]
59 * **Do not compute MSA/conservation scores ?**\ : (boolean) Do not compute Multiple Sequence Alignment and conservation scores ? (MSA scores are computed by default)
60 * **Host taxon ID**\ : (string) Taxon ID of the chassis (default: 83333 [E. coli K12])
61 * **Comma separated taxon IDs of output enzyme sequences**\ : (string) Comma separated taxon IDs of output enzyme sequences
62
63 Output
64 ------
65
66 * **Uniprot IDs (SBML)**\ : Annotated SBML pathway.
67 * **Uniprot IDs (CSV)**\ : Annotated CSV pathway.
68
69 Project Links
70 ------------------
71
72 * `GitHub <https://github.com/brsynth/selenzy-wrapper>`_
73
74 Version
75 ----------
76
77 0.3.0
78
79 Authors
80 -------
81 * **Joan Hérisson**
82
83 License
84 -------
85
86 * `MIT <https://github.com/brsynth/selenzy-wrapper/blob/master/LICENSE>`_
87
88 Acknowledgments
89 ---------------
90
91 * Thomas Duigou
92
93 ]]></help>
94 <citations>
95 <citation type="doi">10.1093/bioinformatics/bty065</citation>
96 </citations>
97 </tool>