Mercurial > repos > iuc > data_manager_fetch_refseq
comparison data_manager/fetch_refseq.xml @ 0:8b91891ae805 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit a572f1f01161527ff6ed4af05bb2e073a8ca903b
author | iuc |
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date | Mon, 01 Oct 2018 15:36:01 -0400 |
parents | |
children | 937f167631b1 |
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1 <tool id="data_manager_fetch_refseq" name="RefSeq data manager" version="0.0.18" tool_type="manage_data"> | |
2 <description>Fetch FASTA data from NCBI RefSeq and update all_fasta data table</description> | |
3 <requirements> | |
4 <requirement type="package">python</requirement> | |
5 <requirement type="package">requests</requirement> | |
6 </requirements> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 python $__tool_directory__/fetch_refseq.py | |
9 #if str( $advanced.advanced_selector ) == 'advanced': | |
10 '${advanced.compress}' | |
11 #end if | |
12 --galaxy_datamanager_filename '${output_file}' | |
13 --division_names ${division_names} | |
14 --mol_types ${mol_types} | |
15 #if str( $pin_date ) != 'NO': | |
16 --pin_date '${pin_date}' | |
17 #end if | |
18 ]]></command> | |
19 <inputs> | |
20 <param argument="division_names" type="select" label="RefSeq division" multiple="true"> | |
21 <option value="archea">Archea</option> | |
22 <option value="bacteria">Bacteria</option> | |
23 <option value="complete">Complete</option> | |
24 <option value="fungi">Fungi</option> | |
25 <option value="invertebrate">Invertebrate</option> | |
26 <option value="mitochondrion">Mitochondrion</option> | |
27 <option value="other">Other</option> | |
28 <option value="plant">Plant</option> | |
29 <option value="plasmid">Plasmid</option> | |
30 <option value="plastid">Plastid</option> | |
31 <option value="protozoa">Protozoa</option> | |
32 <option value="vertebrate_mammalian">Mammalian Vertebrate</option> | |
33 <option value="vertebrate_other">Other Vertebrate</option> | |
34 <option value="viral">Viral</option> | |
35 </param> | |
36 <param argument="mol_types" type="select" multiple="true" label="Molecule type" help="Select at least one of genomic, protein or rna sequence"> | |
37 <option value="protein">Protein</option> | |
38 <option value="genomic">Genomic (DNA)</option> | |
39 <option value="rna">RNA</option> | |
40 </param> | |
41 <conditional name="advanced"> | |
42 <param name="advanced_selector" type="select" label="Advanced Options"> | |
43 <option value="basic" selected="True">Basic</option> | |
44 <option value="advanced">Advanced</option> | |
45 </param> | |
46 <when value="basic"> | |
47 </when> | |
48 <when value="advanced"> | |
49 <param type="boolean" argument="--compress" truevalue="--compress" falsevalue="" label="Compress FASTA files" | |
50 help="Compress downloaded FASTA files (with gzip). Limits compatibility with tools expecting uncompressed FASTA."/> | |
51 </when> | |
52 </conditional> | |
53 <param argument="--pin_date" type="hidden" value="NO" help="Used for testing"/> | |
54 </inputs> | |
55 <outputs> | |
56 <data name="output_file" format="data_manager_json"/> | |
57 </outputs> | |
58 <tests> | |
59 <test> | |
60 <param name="division_names" value="plastid"/> | |
61 <param name="mol_types" value="protein"/> | |
62 <param name="pin_date" value="2018-03-14"/> | |
63 <param name="advanced_selector" value="basic"/> | |
64 <output name="output_file"> | |
65 <assert_contents> | |
66 <has_text text="2018-03-14"/> | |
67 <has_text text="refseq_plastid"/> | |
68 <has_text text="/refseq_plastid."/> | |
69 </assert_contents> | |
70 </output> | |
71 </test> | |
72 </tests> | |
73 <help><![CDATA[ | |
74 This data manager fetches FASTA format collections of proteins, nucleotides (genomic DNA) and RNA | |
75 from NCBI's RefSeq_ data collection. | |
76 | |
77 RefSeq is released every two months and consists of a number of divisions. Some sequences are shared | |
78 between multiple divisions. This data manager allows the Galaxy administrator to select which | |
79 divisions and which molecule types within each division to download. Once downloaded the | |
80 files are made accessible by adding an entry into the *all_fasta* data table. | |
81 | |
82 .. _RefSeq: https://www.ncbi.nlm.nih.gov/refseq/ | |
83 ]]> | |
84 </help> | |
85 <citations> | |
86 <citation type="doi">10.1093/nar/gkv1189</citation> | |
87 </citations> | |
88 </tool> |