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annotate metaquantome_db.xml @ 1:92dc88f0acf1 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
author galaxyp
date Wed, 23 Sep 2020 17:00:20 +0000
parents fe70ad1a3247
children 6f2211aeb393
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fe70ad1a3247 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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1 <tool id="metaquantome_db" name="metaQuantome: database" version="@GVERSION@">
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2 <description>download the GO, EC, and NCBI databases</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 mkdir -p data &&
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9 #set $database_list = str($databases).split(',')
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10 #for $d in $database_list
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11 metaquantome db $d
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12 --dir data &&
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13 #end for
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14 tar --create --file '$outfile' data
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15 ]]></command>
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16 <inputs>
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17 <param name="databases" type="select" multiple="True" display="checkboxes"
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18 label="Databases to Download">
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19 <option value="ncbi" selected="true">NCBI Taxonomy Database</option>
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20 <option value="go" selected="true">Gene Ontology Database</option>
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21 <option value="ec" selected="true">Enzyme Commission (EC) database</option>
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22 </param>
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23 </inputs>
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24 <outputs>
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25 <data format="tar" name="outfile" label="metaquantome databases"/>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="databases" value="go"/>
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30 <output name="outfile">
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31 <assert_contents>
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32 <has_text text="ontology: go"/>
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33 <has_text text="ontology: go/subsets/goslim_metagenomics"/>
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34 </assert_contents>
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35 </output>
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36 </test>
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37 </tests>
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38 <help>
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39 <![CDATA[
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40 metaQuantome database
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41 =====================
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42
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43 metaQuantome uses freely available bioinformatic databases to expand your set of direct annotations.
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44 For most cases, all 3 databases can be downloaded (the default).
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45
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46 The databases are:
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47
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48 1. NCBI taxonomy database. This contains a list of all currently identified taxa and the
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49 relationships between them.
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50
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51 2. Gene Ontology (GO) term database. metaQuantome uses the OBO format of the database. Specifically, two
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52 files are used: the go-basic.obo file, which is a simplified version of the GO database that is guaranteed to be acyclic,
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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
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54 http://geneontology.org/docs/download-ontology/
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56 3. ENZYME database with Enzyme Classification (EC) numbers. This database classifies enzymes and organizes the
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57 relationships between them.
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58
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59 This module downloads the most recent releases of the specified databases and stores them in a single file, which can then
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60 be accessed by the rest of the metaQuantome modules. For reference,
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61 the taxonomy database is the largest (~500 Mb), while the GO and EC databases are smaller: ~34 Mb and ~10Mb, respectively.
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62
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63 Also, note that the databases will be stored in the history so that the date of download can be referenced later.
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64 Thus, the databases will not be modified, except for the NCBI database, which is updated every time ``metaQuantome: expand`` is run (this
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65 is a limitation of the Python package ete3, used within metaQuantome).
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66
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67 Questions, Comments, Problems, Kudos
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68 ------------------------------------
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69
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70 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
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71 ]]></help>
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72 <expand macro="citations" />
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73 </tool>