Mercurial > repos > iuc > data_manager_ncbi_taxonomy_sqlite
comparison data_manager/data_manager_ncbi_taxonomy_sqlite.xml @ 0:7a76cd412252 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
author | iuc |
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date | Tue, 21 Jul 2020 17:04:41 -0400 |
parents | |
children | 54a0869d0051 |
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1 <tool id="data_manager_ncbi_taxonomy_sqlite" name="NCBI Taxonomy SQLite builder" tool_type="manage_data" profile="18.09" version="@PACKAGE_VERSION@+galaxy1" python_template_version="3.5"> | |
2 <macros> | |
3 <token name="@PACKAGE_VERSION@">1.0.5</token> | |
4 </macros> | |
5 <requirements> | |
6 <requirement type="package" version="@PACKAGE_VERSION@">rust-ncbitaxonomy</requirement> | |
7 <requirement type="package" version="3.7">python</requirement> | |
8 </requirements> | |
9 <command detect_errors="exit_code"><![CDATA[ | |
10 #if $taxonomy.taxonomy_source == 'cached': | |
11 #set $taxonomy_dir = $taxonomy.taxonomy_table.fields.path | |
12 #else | |
13 mkdir taxonomy && ln -s '$taxonomy.nodes' taxonomy/nodes.dmp && ln -s '$taxonomy.names' taxonomy/names.dmp && | |
14 #set $taxonomy_dir = 'taxonomy' | |
15 #end if | |
16 python '$__tool_directory__/data_manager_ncbi_taxonomy_sqlite.py' '$taxonomy_dir' '$name' '$description' '$output_file' | |
17 ]]></command> | |
18 <inputs> | |
19 <conditional name="taxonomy"> | |
20 <param name="taxonomy_source" type="select" label="Choose source of NCBI Taxonomy"> | |
21 <option value="cached" selected="true">Use built-in NCBI Taxonomy database</option> | |
22 <option value="history">Datasets from history</option> | |
23 </param> | |
24 <when value="cached"> | |
25 <param type="select" name="taxonomy_table" label="NCBI Taxonomy database"> | |
26 <options from_data_table="ncbi_taxonomy"> | |
27 <filter type="sort_by" column="1" /> | |
28 <validator type="no_options" message="No NCBI Taxonomy downloads are available" /> | |
29 </options> | |
30 <validator type="no_options" message="No NCBI Taxonomy database download is available" /> | |
31 </param> | |
32 </when> | |
33 <when value="history"> | |
34 <param name="nodes" type="data" format="txt" label="NCBI Taxonomy nodes.dmp file" /> | |
35 <param name="names" type="data" format="txt" label="NCBI Taxonomy names.dmp file" /> | |
36 </when> | |
37 </conditional> | |
38 <param name="name" type="text" label="Name of taxonomy database" help="(leave blank to use name based on today's date)" /> | |
39 <param name="description" type="text" label="Description of taxonomy database" help="(leave blank to use name based on today's date)" /> | |
40 </inputs> | |
41 <outputs> | |
42 <data name="output_file" format="data_manager_json"/> | |
43 </outputs> | |
44 <tests> | |
45 <test> | |
46 <conditional name="taxonomy"> | |
47 <param name="taxonomy_source" value="history" /> | |
48 <param name="nodes" ftype="txt" value="taxdb/nodes.dmp" /> | |
49 <param name="names" ftype="txt" value="taxdb/names.dmp" /> | |
50 </conditional> | |
51 <param name="name" value="test" /> | |
52 <param name="description" value="test database" /> | |
53 <output name="output_file"> | |
54 <assert_contents> | |
55 <has_text text="tax.ncbitaxonomy.sqlite" /> | |
56 <has_text text="test database" /> | |
57 </assert_contents> | |
58 </output> | |
59 </test> | |
60 <test> | |
61 <conditional name="taxonomy"> | |
62 <param name="taxonomy_source" value="cached" /> | |
63 <param name="taxonomy_table" value="sample" /> | |
64 </conditional> | |
65 <param name="name" value="test" /> | |
66 <param name="description" value="test database" /> | |
67 <output name="output_file"> | |
68 <assert_contents> | |
69 <has_text text="tax.ncbitaxonomy.sqlite" /> | |
70 <has_text text="test database" /> | |
71 </assert_contents> | |
72 </output> | |
73 </test> | |
74 </tests> | |
75 <help><![CDATA[ | |
76 The data manager creates a SQLite version the NCBI Taxonomy database, using the plain text files of the | |
77 NCBI database as input. Storing the database as a SQLite database allows for faster querying. | |
78 | |
79 Input is either from the individual files (nodes.dmp and names.dmp) from the NCBI Taxonomy database or | |
80 from a previously downloaded code of the database stored as "reference data" in the Galaxy server. | |
81 | |
82 .. class: infomark | |
83 | |
84 *Notice:** If you leave name, or description blank, it will be generated automatically from the current date. | |
85 ]]></help> | |
86 <citations> | |
87 <citation type="bibtex">@misc{vanHeusen2020, | |
88 author = {van Heusden, P.}, | |
89 title = {a Rust crate for working with a local copy of the NCBI Taxonomy database }, | |
90 year = {2020}, | |
91 publisher = {GitHub}, | |
92 journal = {GitHub repository}, | |
93 howpublished = {\url{https://github.com/pvanheus/ncbitaxonomy}}, | |
94 commit = {84d79cdcf2adb262c61511f8c7b9eceb5299b87d} | |
95 } | |
96 </citation> | |
97 </citations> | |
98 </tool> |