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
date Mon, 06 Nov 2017 06:21:50 -0500
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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>