Mercurial > repos > iuc > checkm2_build_database

comparison data_manager/checkm2_datamanager.xml @ 0:34dc5b5f35ca draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit f02ef28c39a18da4afb9148d0342244f6788485a
author iuc
date Tue, 14 Jan 2025 20:26:31 +0000
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children 757826aa89c3
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-1:000000000000 0:34dc5b5f35ca
1 <tool id="checkm2_build_database" name="CheckM2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>database builder</description>
3 <macros>
4 <!-- on update run a local test setting `test` to something else than "true" -->
5 <token name="@TOOL_VERSION@">1.0.2</token>
6 <token name="@VERSION_SUFFIX@">0</token>
7 <token name="@PROFILE@">23.1</token>
8 </macros>
9 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">checkm2</requirement>
11 </requirements>
12 <version_command>checkm2 --version</version_command>
13 <command detect_errors="exit_code"><![CDATA[
14 mkdir -p '$out_file.extra_files_path' &&
15 #if $test != "true"
16 checkm2 database --download --path '$out_file.extra_files_path'/ &&
17 mv '$out_file.extra_files_path'/CheckM2_database/uniref100.KO.1.dmnd '$out_file.extra_files_path' &&
18 #else
19 touch '$out_file.extra_files_path'/uniref100.KO.1.dmnd &&
20 #end if
21 cp '$dmjson' '$out_file'
22 ]]></command>
23 <configfiles>
24 <configfile name="dmjson"><![CDATA[
25 {
26 "data_tables":{
27 "checkm2":[
28 {
29 "path":"uniref100.KO.1.dmnd",
30 "name":"CheckM2 diamond DB downloaded with version @TOOL_VERSION@",
31 "version":"@TOOL_VERSION@",
32 "value":"@TOOL_VERSION@"
33 }
34 ]
35 }
36 }]]>
37 </configfile>
38 </configfiles>
39 <inputs>
40 <param name="test" type="hidden"/>
41 </inputs>
42 <outputs>
43 <data name="out_file" format="data_manager_json" />
44 </outputs>
45 <tests>
46 <test expect_num_outputs="1">
47 <param name="test" value="true"/>
48 <output name="out_file">
49 <assert_contents>
50 <has_text text='"value":"@TOOL_VERSION@"'/>
51 <has_text text='"name":"CheckM2 diamond DB downloaded with version @TOOL_VERSION@"'/>
52 </assert_contents>
53 </output>
54 </test>
55 </tests>
56 <help><![CDATA[
57 Download and extract CheckM2 reference data.
58 ]]></help>
59 <citations>
60 <citation type="doi">10.1038/s41592-023-01940-w</citation>
61 </citations>
62 </tool>