annotate ete_init_taxdb.xml @ 16:e4d5d9a69c9d draft default tip

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit a0d7ab86b86bb764e457767bf8e8bc29868d0cbb

1 <tool id="ete_init_taxdb" name="ETE taxa DB generator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2     <description>generates the ETE sqlite DB from the NCBI taxdump.tar.gz</description>
3     <macros>
4         <import>ete_macros.xml</import>
5     </macros>
6     <expand macro="bio_tools"/>
7     <expand macro="requirements" />
8     <command detect_errors="exit_code"><![CDATA[
9 python '$__tool_directory__/ete_init_taxdb.py'
10 #if $latestcond.latest == "local"
11     -t '$latestcond.taxdump'
12 #end if
13 -d '$database'
14     ]]></command>
15     <inputs>
16         <conditional name="latestcond">
17             <param name="latest" type="select" label="Get latest version" help="Get the latest version of the taxdump from the NCBI website">
18                 <option value="local" selected="true">Use a local taxdump</option>
19                 <option value="latest">Get latest taxdump online</option>
20             </param>
21             <when value="local">
22                 <param name="taxdump" type="data" format="tar" label="NCBI taxdump" help="NCBI taxonomy database dump in tar.gz format" />
23             </when>
24             <when value="latest" />
25         </conditional>
26     </inputs>
27     <outputs>
28         <data name="database" format="sqlite" label="${tool.name} on ${on_string}" />
29     </outputs>
30     <tests>
31         <test>
32             <conditional name="latestcond">
33                 <param name="latest" value="local" />
34                 <param name="taxdump" ftype="tar" value="taxdump.tar.gz" />
35             </conditional>
36             <output name="database" file="taxdump.sqlite" compare="sim_size" />
37         </test>
38     </tests>
39     <help><![CDATA[
40 Generates the ETE sqlite data base from the NCBI taxdump.tar.gz using the `ETE Toolkit`_.
41 
42 .. _ETE Toolkit: https://etetoolkit.org/
43 
44 **Input**
45 
46 - NCBI taxdump: NCBI taxdump in tar.gz format. If not given the latest is downloaded from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
47 
48 **Output**
49 
50 - *(ETE3) Taxonomy Database* a sqlite database that has been created by ETE from the NCBI taxonomy dump
51     ]]></help>
52     <expand macro="citations" />
53 </tool>