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comparison data_manager/pangolin_data_dm.xml @ 0:40c380ea283f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
author iuc
date Wed, 20 Jul 2022 21:02:02 +0000
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children f0214079e0c7
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-1:000000000000 0:40c380ea283f
1 <tool id="data_manager_pangolin_data" name="pangolin-data data manager" version="0.0.1+galaxy0" tool_type="manage_data" profile="20.01">
2 <requirements>
3 <requirement type="package">python</requirement>
4 <requirement type="package" version="22.1.2">pip</requirement>
5 <requirement type="package" version="2.28.1">requests</requirement>
6 <requirement type="package" version="2.37.1">git</requirement>
7 <requirement type="package" version="3.2.0">git-lfs</requirement>
8 <requirement type="package" version="3.1.27">gitpython</requirement>
9 </requirements>
10 <macros>
11 <import>macros.xml</import>
12 </macros>
13 <command detect_errors="exit_code"><![CDATA[
14 #set $dt_names = []
15 #if str($pangolin_data.enable) == "latest" or str($pangolin_data.enable) == "versions"
16 #set $dt_names = $dt_names + ["pangolin_data"]
17 #end if
18 #if str($pangolin_constellations.enable) == "latest" or str($pangolin_constellations.enable) == "versions"
19 #set $dt_names = $dt_names + ["pangolin_constellations"]
20 #end if
21 #if str($pangolin_assignment.enable) == "latest" or str($pangolin_assignment.enable) == "versions"
22 #set $dt_names = $dt_names + ["pangolin_assignment"]
23 #end if
24 #for $dt_name in $dt_names
25 #set $data_table = $__app__.tool_data_tables.get($dt_name)
26 #if $data_table is not None and len($data_table.get_fields()) != 0
27 #set $known_revisions = '--known_revisions=' + ','.join([row[0] for row in $data_table.get_fields()])
28 #else
29 #set $known_revisions = ''
30 #end if
31 python '$__tool_directory__/pangolin_data_dm.py'
32 $known_revisions
33 #if $getVar($dt_name).enable == "latest"
34 --latest
35 #else if $getVar($dt_name).enable == "versions"
36 --version_compatibility_file '$getVar($dt_name).compatibility_file'
37 --versions=$getVar($dt_name).versions
38 #end if
39 '$dt_name'
40 datatable_cache.json
41 '${output_file}' &&
42 #end for
43 cp datatable_cache.json '${output_file}'
44 ]]></command>
45 <inputs>
46 <expand macro="download_conditional" dt_name="pangolin_data" database_name="pangolin-data" software_name="pangolin" />
47 <expand macro="download_conditional" dt_name="pangolin_constellations" database_name="constellations" software_name="scorpio" />
48 <expand macro="download_conditional" dt_name="pangolin_assignment" database_name="pangolin-assignment" software_name="pangolin" />
49 </inputs>
50 <outputs>
51 <data name="output_file" format="data_manager_json"/>
52 </outputs>
53 <tests>
54 <test expect_num_outputs="1">
55 <conditional name="pangolin_data">
56 <param name="enable" value="versions" />
57 <param name="compatibility_file" ftype="csv" value="data_compatibility.csv" />
58 <param name="versions" value="1.12" />
59 </conditional>
60 <conditional name="pangolin_constellations">
61 <param name="enable" value="versions" />
62 <param name="compatibility_file" ftype="csv" value="data_compatibility.csv" />
63 <param name="versions" value="0.1.10" />
64 </conditional>
65 <conditional name="pangolin_assignment">
66 <param name="enable" value="no" />
67 </conditional>
68 <output name="output_file">
69 <assert_contents>
70 <has_text text="pangolin-data v1.12" />
71 <has_text text='"description": "constellations release v0.1.10"' />
72 <has_text text='"min_scorpio_version": "0.3.17"' />
73 <not_has_text text='"description": "pangolin-assignment' />
74 </assert_contents>
75 </output>
76 </test>
77 <test expect_num_outputs="1">
78 <conditional name="pangolin_data">
79 <param name="enable" value="no" />
80 </conditional>
81 <conditional name="pangolin_constellations">
82 <param name="enable" value="no" />
83 </conditional>
84 <conditional name="pangolin_assignment">
85 <param name="enable" value="versions" />
86 <param name="compatibility_file" ftype="csv" value="data_compatibility.csv" />
87 <param name="versions" value="1.12" />
88 </conditional>
89 <output name="output_file">
90 <assert_contents>
91 <has_text text='"value": "v1.12"' />
92 <has_text text='"min_pangolin_version": "4"' />
93 <not_has_text text='"description": "constellations' />
94 <not_has_text text='"description": "pangolin-data' />
95 </assert_contents>
96 </output>
97 </test>
98 <test expect_failure="true">
99 <conditional name="pangolin_data">
100 <param name="enable" value="no" />
101 </conditional>
102 <conditional name="pangolin_constellations">
103 <param name="enable" value="no" />
104 <param name="compatibility_file" ftype="csv" value="data_compatibility.csv" />
105 <param name="versions" value="0.0.40" />
106 </conditional>
107 <conditional name="pangolin_assignment">
108 <param name="enable" value="no" />
109 </conditional>
110 </test>
111 </tests>
112 <help><![CDATA[
113 This data managers fetches models (from the pangolin-data_,
114 pangolin-assignment_ and constellations_ repositories) for the
115 pangolin_ SARS-CoV-2 lineage typing tool and updates the pangolin_data,
116 pangolin_assignment and pangolin_constellations data tables.
117
118 The default is to fetch the latest version of the databases. If specific versions of databases
119 need to be installed, a version compatibility matrix needs to be provided to help choose
120 the versions available. This matrix is stored in a CSV file in the pangolin repository
121 and can be downloaded at this link_. When loading this file into Galaxy, the csv datatype
122 needs to be selected, because the automatic format detection code detects this file as type txt.
123
124 **Note** that this data manager will only download database versions mentioned in the above
125 mentioned file. While effort is taken to ensure that this file is updated with each pangolin
126 database release, if that has not happened, the user of this data manager will need to provide
127 their own version compatibility matrix file in order to load the latest database release into Galaxy.
128
129 The data manager will read the existing data tables and not re-download or replace databases
130 that are already present in those data tables.
131
132 .. _pangolin-data: https://github.com/cov-lineages/pangolin-data
133 .. _pangolin-assignment: https://github.com/cov-lineages/pangolin-assignment
134 .. _constellations: https://github.com/cov-lineages/constellations
135 .. _pangolin: https://github.com/cov-lineages/pangolin
136 .. _link: https://raw.githubusercontent.com/cov-lineages/pangolin/master/pangolin/data/data_compatibility.csv
137 ]]></help>
138 <citations>
139 <citation type="doi">10.1093/ve/veab064</citation>
140 </citations>
141 </tool>