Mercurial > repos > iuc > data_manager_primer_scheme_bedfiles
comparison data_manager/install_primer_scheme_bedfiles.xml @ 0:ae730ecdc7e7 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
author | iuc |
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date | Sun, 19 Apr 2020 09:22:19 -0400 |
parents | |
children | cce5d9327cd6 |
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1 <tool id="data_manager_primer_scheme_bedfiles" name="BED-format primer scheme data manager" version="0.0.8" tool_type="manage_data" profile="19.05"> | |
2 <requirements> | |
3 <requirement type="package">python</requirement> | |
4 <requirement type="package" version="2.22.0">requests</requirement> | |
5 </requirements> | |
6 <!-- fetch all the primers in one go --> | |
7 <command detect_errors="exit_code"> | |
8 python '$__tool_directory__/install_primer_scheme_bedfiles.py' | |
9 '${output_file}' | |
10 #if $input.input_type == "ARTIC" | |
11 --artic_primers '${input.primers}' | |
12 #else | |
13 --primer_file '${input.primer_input}' | |
14 --primer_name '${input.primer_name}' | |
15 --primer_description '${input.primer_description}' | |
16 #end if | |
17 </command> | |
18 <inputs> | |
19 <conditional name="input"> | |
20 <param name="input_type" label="Choose the source for primer schemes" type="select"> | |
21 <option value="ARTIC" selected="true">ARTIC SARS-CoV-2 Github page</option> | |
22 <option value="history">History</option> | |
23 </param> | |
24 <when value="ARTIC"> | |
25 <param name="primers" type="select" multiple="true" label="SARS-CoV-2 Primers to fetch"> | |
26 <option value="ARTICv1" selected="true">ARTIC v1</option> | |
27 <option value="ARTICv2" selected="true">ARTIC v2</option> | |
28 <option value="ARTICv3" selected="true">ARTIC v3</option> | |
29 </param> | |
30 </when> | |
31 <when value="history"> | |
32 <param name="primer_input" label="Select history item" type="data" format="bed" /> | |
33 <param name="primer_name" label="Name for this primer scheme" type="text" | |
34 help="Non-word characters will be removed from primer scheme name and spaces replaced with underscore (_)" /> | |
35 <param name="primer_description" label="Description for primer scheme" type="text" /> | |
36 </when> | |
37 </conditional> | |
38 </inputs> | |
39 <outputs> | |
40 <data name="output_file" format="data_manager_json"/> | |
41 </outputs> | |
42 <tests> | |
43 <test> | |
44 <param name="input_type" value="ARTIC" /> | |
45 <param name="primers" value="ARTICv1,ARTICv2,ARTICv3"/> | |
46 <output name="output_file"> | |
47 <assert_contents> | |
48 <has_text text="ARTIC"/> | |
49 </assert_contents> | |
50 </output> | |
51 </test> | |
52 <test> | |
53 <param name="input_type" value="history" /> | |
54 <param name="primer_input" ftype="bed" value="sample1.bed" /> | |
55 <param name="primer_name" value="sample_primer" /> | |
56 <param name="primer_description" value="sample primer scheme" /> | |
57 <output name="output_file"> | |
58 <assert_contents> | |
59 <has_text text="sample_primer"/> | |
60 </assert_contents> | |
61 </output> | |
62 </test> | |
63 </tests> | |
64 </tool> |