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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
author iuc
date Wed, 25 Sep 2024 14:12:11 +0000
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1 <tool id="chewbbaca_downloadschema" name="chewBBACA DownloadSchema" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Download a schema from Chewie-NS</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 chewBBACA.py DownloadSchema
9 -sp $species_id
10 -sc $schema_id
11 -o 'output' &&
12 ## The output is named based on the species name. Rename it to schema_seed so it is compatible for other chewbbaca tools.
13 mv output/* 'schema_seed' &&
14 zip -r schema_seed.zip 'schema_seed'
15 ]]></command>
16 <inputs>
17 <param argument="--species-id" type="select" label="Species ID">
18 <option value="1">Streptococcus pyogenes</option>
19 <option value="2">Acinetobacter baumannii</option>
20 <option value="3">Arcobacter butzleri</option>
21 <option value="4">Campylobacter jejuni</option>
22 <option value="5">Escherichia coli</option>
23 <option value="6">Listeria monocytogenes</option>
24 <option value="7">Yersinia enterocolitica</option>
25 <option value="8">Salmonella enterica</option>
26 <option value="9">Streptococcus agalactiae</option>
27 <option value="10">Brucella melitensis</option>
28 <option value="11">Brucella</option>
29 <option value="12">Clostridium perfringens</option>
30 <option value="13">Clostridium chauvoei</option>
31 <option value="14">Bacillus anthracis</option>
32 <option value="15">Klebsiella oxytoca</option>
33 <option value="16">Clostridium neonatale</option>
34 </param>
35 <!-- Currently,the schema id can only be set to 1. Maybe in the next versions other values possible -->
36 <param argument="--schema-id" type="integer" min="1" value="1" label="Schema ID"/>
37 </inputs>
38 <outputs>
39 <data format="zip" name="schema" from_work_dir="schema_seed.zip" label="${tool.name} Schema files"/>
40 </outputs>
41 <tests>
42 <test expect_exit_code="0">
43 <param name="species_id" value="13"/>
44 <param name="schema_id" value="1"/>
45 <assert_stdout>
46 <has_text text="Schema is now available at"/>
47 <has_text text="Finished at"/>
48 </assert_stdout>
49 <output name="schema">
50 <assert_contents>
51 <has_archive_member path="schema_seed/.*\.fasta" n="4446"/>
52 <has_archive_member path="schema_seed/short/.*\.fasta" n="2223"/>
53 <has_archive_member path="schema_seed/\.ns_config"/>
54 <has_archive_member path="schema_seed/\.schema_config"/>
55 </assert_contents>
56 </output>
57 </test>
58 </tests>
59 <help>
60
61 chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
62
63 The DownloadSchema module enables the download of schemas from the Chewie-NS server.
64
65
66 .. class:: infomark
67
68 **Note**
69
70 The output schema files are in a zip file. This file can be used as input for other chewBBACA tools.
71
72 -----
73
74 Compressed versions of every schema in the Chewie-NS are also available for download:
75 - through the `Chewie-NS public website`_
76 - through the (/species/{species_id}/schemas/{schema_id}/zip) API endpoint in Swagger_
77 - with a simple curl command (e.g.: curl -X GET "https://chewbbaca.online/NS/api/species/9/schemas/1/zip?request_type=download" -H "accept: application/json")
78
79 .. _Chewie-NS public website: https://chewbbaca.online/
80 .. _Swagger: https://chewbbaca.online/api/NS/api/docs
81 </help>
82 <expand macro="citations" />
83 </tool>