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