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comparison ete_init_taxdb.xml @ 2:03c10736e497 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
author earlhaminst
date Tue, 07 Nov 2017 11:45:13 -0500
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1:a4ba317fc713 2:03c10736e497
1 <tool id="ete_init_taxdb" name="ETE taxa DB generator" version="@VERSION@">
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="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 python '$__tool_directory__/ete_init_taxdb.py'
9 #if $latestcond.latest == "local"
10 -t '$latestcond.taxdump'
11 #end if
12 -d '$database'
13 ]]></command>
14 <inputs>
15 <conditional name="latestcond">
16 <param name="latest" type="select" label="Get latest version" help="Get the latest version of the taxdump from the NCBI website">
17 <option value="local" selected="true">Use a local taxdump</option>
18 <option value="latest">Get latest taxdump online</option>
19 </param>
20 <when value="local">
21 <param name="taxdump" type="data" format="tar" label="NCBI taxdump" help="NCBI taxonomy database dump in tar.gz format" />
22 </when>
23 <when value="latest" />
24 </conditional>
25 </inputs>
26 <outputs>
27 <data name="database" format="sqlite" label="${tool.name} on ${on_string}" />
28 </outputs>
29 <tests>
30 <test>
31 <param name="latest" value="local" />
32 <param name="taxdump" ftype="tar" value="taxdump.tar.gz" />
33 <output name="database" file="taxdump.sqlite" compare="sim_size" />
34 </test>
35 </tests>
36 <help><![CDATA[
37 Generates the ETE sqlite data base from the NCBI taxdump.tar.gz using the .. _ETE Toolkit: http://etetoolkit.org/
38
39 **Input**
40
41 - 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
42
43 **Output**
44
45 - *(ETE3) Taxonomy Database* a sqlite database that has been created by ETE from the NCBI taxonomy dump
46 ]]></help>
47 <expand macro="citations" />
48 </tool>