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comparison metaquantome_db.xml @ 0:f1834b310c09 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
author galaxyp
date Thu, 25 Apr 2019 13:47:16 -0400
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1 <tool id="metaquantome_db" name="metaQuantome: database" version="@GVERSION@">
2 <description>download the GO, EC, and NCBI databases</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 mkdir -p data &&
9 #set $database_list = str($databases).split(',')
10 #for $d in $database_list
11 metaquantome db $d
12 --dir data &&
13 #end for
14 tar --create --file '$outfile' data
15 ]]></command>
16 <inputs>
17 <param name="databases" type="select" multiple="True" display="checkboxes"
18 label="Databases to Download">
19 <option value="ncbi" selected="true">NCBI Taxonomy Database</option>
20 <option value="go" selected="true">Gene Ontology Database</option>
21 <option value="ec" selected="true">Enzyme Commission (EC) database</option>
22 </param>
23 </inputs>
24 <outputs>
25 <data format="tar" name="outfile" label="metaquantome databases"/>
26 </outputs>
27 <tests>
28 <test>
29 <param name="databases" value="go"/>
30 <output name="outfile">
31 <assert_contents>
32 <has_text text="ontology: go"/>
33 <has_text text="ontology: go/subsets/goslim_metagenomics"/>
34 </assert_contents>
35 </output>
36 </test>
37 </tests>
38 <help>
39 <![CDATA[
40 metaQuantome database
41 =====================
42
43 metaQuantome uses freely available bioinformatic databases to expand your set of direct annotations.
44 For most cases, all 3 databases can be downloaded (the default).
45
46 The databases are:
47
48 1. NCBI taxonomy database. This contains a list of all currently identified taxa and the
49 relationships between them.
50
51 2. Gene Ontology (GO) term database. metaQuantome uses the OBO format of the database. Specifically, two
52 files are used: the go-basic.obo file, which is a simplified version of the GO database that is guaranteed to be acyclic,
53 and the metagenomics slim GO, which is a subset of the full GO that is useful for microbiome research. More details are available at
54 http://geneontology.org/docs/download-ontology/
55
56 3. ENZYME database with Enzyme Classification (EC) numbers. This database classifies enzymes and organizes the
57 relationships between them.
58
59 This module downloads the most recent releases of the specified databases and stores them in a single file, which can then
60 be accessed by the rest of the metaQuantome modules. For reference,
61 the taxonomy database is the largest (~500 Mb), while the GO and EC databases are smaller: ~34 Mb and ~10Mb, respectively.
62
63 Also, note that the databases will be stored in the history so that the date of download can be referenced later.
64 Thus, the databases will not be modified, except for the NCBI database, which is updated every time ``metaQuantome: expand`` is run (this
65 is a limitation of the Python package ete3, used within metaQuantome).
66
67 Questions, Comments, Problems, Kudos
68 ------------------------------------
69
70 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
71 ]]></help>
72 <expand macro="citations" />
73 </tool>