Mercurial > repos > ufz > data_manager_dfast

comparison data_manager/dfast.xml @ 0:a3ef2075f00e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_dfast commit ceec7eb1afdcdebbbc145e7fe9fa5a38dafcd9b0
author ufz
date Wed, 16 Apr 2025 10:58:35 +0000
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children 23aec9361162
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-1:000000000000 0:a3ef2075f00e
1 <tool id="data_manager_dfast" name="DFAST data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
2 <macros>
3 <token name="@TOOL_VERSION@">1.3.6</token>
4 <token name="@VERSION_SUFFIX@">0</token>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">dfast</requirement>
8 </requirements>
9 <version_command>dfast --version | cut -d" " -f3</version_command>
10 <command detect_errors="exit_code"><![CDATA[
11 mkdir '$output_file.extra_files_path' &&
12 wget https://dfast.annotation.jp/dfast_core_db.tar.gz &&
13 tar -xvf dfast_core_db.tar.gz &&
14 mv db/* '$output_file.extra_files_path'/ &&
15 cp '$dmjson' '$output_file'
16 ]]></command>
17 <configfiles>
18 <configfile name="dmjson"><![CDATA[
19 #from datetime import datetime
20 #set version_id=datetime.now().strftime("%Y-%m-%d-%H%M%S")
21 {
22 "data_tables":{
23 "dfast":[
24 {
25 "value":"$version_id",
26 "description":"DFAST DB from $version_id",
27 "version":"$version_id",
28 "path":"$output_file.extra_files_path"
29 }
30 ]
31 }
32 }]]></configfile>
33 </configfiles>
34 <inputs>
35 <param name="wget" type="boolean" truevalue="--wget" falsevalue="" checked="False" label="Download using wget" help="Try this if you get certificate errors"/>
36 </inputs>
37 <outputs>
38 <data name="output_file" format="data_manager_json"/>
39 </outputs>
40 <tests>
41 <test>
42 <output name="output_file">
43 <assert_contents>
44 <has_text text="DFAST DB"/>
45 <has_text text="dfast"/>
46 </assert_contents>
47 </output>
48 </test>
49 </tests>
50 <help><![CDATA[
51 This data managers fetches DFAST reference data from https://dfast.annotation.jp/
52 ]]></help>
53 <citations>
54 <citation type="doi">10.5281/zenodo.4054262</citation>
55 </citations>
56 </tool>