Mercurial > repos > iuc > data_manager_mothur_toolsuite
comparison data_manager/data_manager_fetch_mothur_reference_data.xml @ 0:ab7a7e798c34 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
author | iuc |
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date | Mon, 06 Nov 2017 06:21:50 -0500 |
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children | aec831b54a5b |
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1 <?xml version="1.0"?> | |
2 <tool id="data_manager_fetch_mothur_reference_data" name="Fetch Mothur toolsuite reference data" version="0.1.3" tool_type="manage_data"> | |
3 <description>Fetch and install reference data for Mothur</description> | |
4 <requirements> | |
5 <requirement type="package" version="2.7">python</requirement> | |
6 </requirements> | |
7 <command><![CDATA[ | |
8 python '$__tool_directory__/fetch_mothur_reference_data.py' | |
9 --source=$data_source.data_source_selector | |
10 #if str( $data_source.data_source_selector ) == "mothur_website" | |
11 --datasets '${data_source.ref_data}' | |
12 #elif str( $data_source.data_source_selector ) == "filesystem_paths" | |
13 --description '${data_source.description}' | |
14 --paths '${data_source.paths}' | |
15 #if $data_source.create_symlink | |
16 --link | |
17 #end if | |
18 #end if | |
19 '${out_file}' | |
20 ]]></command> | |
21 <inputs> | |
22 <conditional name="data_source"> | |
23 <param name="data_source_selector" type="select" | |
24 label="Choose the source for the reference data"> | |
25 <option value="mothur_website">Mothur website</option> | |
26 <option value="filesystem_paths">Filesystem paths</option> | |
27 </param> | |
28 <when value="mothur_website"> | |
29 <param name="ref_data" type="select" display="checkboxes" multiple="true" | |
30 label="Reference dataset to install"> | |
31 <option value="lookup_titanium">GS FLX Titanium lookup files</option> | |
32 <option value="lookup_gsflx">GSFLX lookup files</option> | |
33 <option value="lookup_gs20">GS20 lookup files</option> | |
34 <option value="RDP_v16">RDP reference files (training set version 16)</option> | |
35 <option value="RDP_v14">RDP reference files (training set version 14)</option> | |
36 <option value="RDP_v10">RDP reference files (training set version 10)</option> | |
37 <option value="RDP_v9">RDP reference files (training set version 9)</option> | |
38 <option value="RDP_v7">RDP reference files (training set version 7)</option> | |
39 <option value="RDP_v6">RDP reference files (training set version 6)</option> | |
40 <option value="silva_release_128">SILVA reference files (release 128)</option> | |
41 <option value="silva_release_123">SILVA reference files (release 123)</option> | |
42 <option value="silva_release_119">SILVA reference files (release 119)</option> | |
43 <option value="silva_release_102">SILVA reference files (release 102)</option> | |
44 <option value="greengenes_August2013">Greengenes reference taxonomy and alignment v13.8 (August 2013)</option> | |
45 <option value="greengenes_May2013">Greengenes reference taxonomy and alignment v13.5 (May 2013)</option> | |
46 <option value="greengenes_old">Greengenes reference taxonomy and alignment (pre-May 2013)</option> | |
47 <option value="greengenes_gold_alignment">Greengenes gold alignment</option> | |
48 <option value="secondary_structure_maps_silva">SILVA secondary structure maps</option> | |
49 <option value="secondary_structure_maps_greengenes">Greengenes secondary structure maps</option> | |
50 </param> | |
51 </when> | |
52 <when value="filesystem_paths"> | |
53 <param name="description" type="text" value="" size="50" | |
54 label="Description of the data" optional="False" /> | |
55 <param name="paths" type="text" value="" area="True" size="10x50" | |
56 label="Paths to upload" optional="False" | |
57 help="Upload all files pasted in the box. The (recursive) contents of any pasted directories will be added as well." /> | |
58 <param type="boolean" name="create_symlink" truevalue="create_symlink" | |
59 falsevalue="copy_file" | |
60 label="Create symlinks to data instead of copying into Galaxy" checked="on" /> | |
61 </when> | |
62 </conditional> | |
63 </inputs> | |
64 <outputs> | |
65 <data name="out_file" format="data_manager_json" /> | |
66 </outputs> | |
67 <tests> | |
68 <test> | |
69 <param name="data_sourece|ref_data" value="lookup_titanium"/> | |
70 <output name="out_file"> | |
71 <assert_contents> | |
72 <has_text text="GS FLX Titanium" /> | |
73 <has_text text="LookUp_Titanium.pat" /> | |
74 </assert_contents> | |
75 </output> | |
76 </test> | |
77 </tests> | |
78 <help> | |
79 .. class:: infomark | |
80 | |
81 **What it does** | |
82 | |
83 This tool fetches reference data used by the mothur_toolsuite set of Galaxy tools, | |
84 and populates the appropriate data tables. | |
85 | |
86 The reference data can be imported directly from the Mothur website, or from files | |
87 in a server directory. | |
88 | |
89 Files are added to the following data tables based on file extension: | |
90 | |
91 * **mothur_lookup**: for .pat files | |
92 * **mothur_aligndb**: for .fasta files | |
93 * **mothur_map**: for .map files | |
94 * **mothur_taxonomy**: for .tax files | |
95 | |
96 ------ | |
97 | |
98 **Importing from Mothur website** | |
99 | |
100 Reference data sets provided by the Mothur developers can be downloaded from the | |
101 Mothur website. See the following pages to get more information about each dataset: | |
102 | |
103 * Lookup data: http://www.mothur.org/wiki/Lookup_files | |
104 * RDP reference data: http://www.mothur.org/wiki/RDP_reference_files | |
105 * Silva data: http://www.mothur.org/wiki/Silva_reference_files | |
106 * Greengenes data: http://www.mothur.org/wiki/Greengenes-formatted_databases | |
107 * Secondary structure maps: http://www.mothur.org/wiki/Secondary_structure_map | |
108 | |
109 **Importing from file system paths** | |
110 | |
111 If reference data is already on the server filesystem then use this option to | |
112 import it into the Mothur data tables. The appropriate data tables are determined | |
113 based on the file extensions. | |
114 | |
115 Optionally a description can be added which will appear next to the base of the | |
116 reference file name in the data table entry. | |
117 | |
118 ------ | |
119 | |
120 .. class:: warningmark | |
121 | |
122 **A note on Lane masks** | |
123 | |
124 Lane mask data is also available via the Mothur website (files ending in ".filter"): | |
125 | |
126 * http://www.mothur.org/wiki/Lane_mask | |
127 | |
128 but as these data are not currently used in the toolsuite, they cannot be imported | |
129 using this data manager. | |
130 | |
131 </help> | |
132 </tool> |