Mercurial > repos > iuc > data_manager_fetch_busco

comparison data_manager/busco_fetcher.xml @ 8:29548c43fb33 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
author iuc
date Tue, 22 Apr 2025 13:11:38 +0000
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7:83c7f3907ad2 8:29548c43fb33
1 <tool id="busco_fetcher" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="23.1">
2 <description>dataset dowloader</description>
3 <macros>
4 <token name="@TOOL_VERSION@">5.8.0</token>
5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 busco --download_path '$out_file.extra_files_path' --download '$lineage' &&
12 ## remove unwanted lineage folders and placement files
13 ## https://gitlab.com/ezlab/busco/-/issues/784
14 if [ -d '$out_file.extra_files_path'/lineages ]; then
15 find '$out_file.extra_files_path'/lineages/ -mindepth 1 -maxdepth 1 ! -name '*_$datasets_version*' -exec rm -rf {} \;;
16 fi &&
17 if [ -d '$out_file.extra_files_path'/placement_files ]; then
18 find '$out_file.extra_files_path'/placement_files/ -mindepth 1 -maxdepth 1 ! -name '*_$datasets_version*' -delete;
19 fi &&
20 ## unpack faa.gz files ready to use
21 ## https://gitlab.com/ezlab/busco/-/issues/789
22 if [ -d '$out_file.extra_files_path'/lineages ]; then
23 find '$out_file.extra_files_path'/lineages/ -name "*.faa.gz" -exec gunzip {} \;;
24 fi
25 && cp '$dmjson' '$out_file'
26 ]]></command>
27 <configfiles>
28 <configfile name="dmjson"><![CDATA[
29 #from datetime import datetime
30 {
31 "data_tables":{
32 "busco_database":[
33 {
34 "value":"$lineage $datasets_version #echo datetime.now().strftime('%Y-%m-%d-%H%M%S')#",
35 "name":"$lineage $datasets_version #echo datetime.now().strftime('%Y-%m-%d-%H%M%S')#",
36 "version":"@TOOL_VERSION@",
37 "path":"$out_file.extra_files_path"
38 }
39 ]
40 }
41 }]]>
42 </configfile>
43 </configfiles>
44 <inputs>
45 <param name="lineage" argument="--download" type="select" label="Select the lineage to be downloaded">
46 <option value="all">All</option>
47 <option value="prokaryota">Prokaryota</option>
48 <option value="eukaryota">Eukaryota</option>
49 <option value="virus">Virus</option>
50 </param>
51 <param argument="--datasets_version" type="select" label="OrthoDB version" help="By March 2025 OrthoDB 12 datasets were only available for Prokaryota (https://busco-data2.ezlab.org/v5/data/)">
52 <option value="odb10" selected="true">OrthoDB 10</option>
53 <option value="odb12">OrthoDB 12</option>
54 </param>
55 </inputs>
56 <outputs>
57 <data name="out_file" format="data_manager_json" label="BUSCO data manager: JSON"/>
58 </outputs>
59 <tests>
60 <test expect_num_outputs="1">
61 <param name="lineage" value="virus"/>
62 <output name="out_file">
63 <assert_contents>
64 <has_text text="virus"/>
65 <has_text text="5.8.0"/>
66 </assert_contents>
67 </output>
68 </test>
69 </tests>
70 <help>This tool downloads the BUSCO databases.</help>
71 <citations>
72 <citation type="doi">10.1093/bioinformatics/btv351</citation>
73 </citations>
74 </tool>