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comparison data_manager/gtdbtk_database_installer.xml @ 7:05f85f5bfc48 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 671e8c706fa211b6ec1c476d3d1a36d098822fe5
author iuc
date Thu, 03 Oct 2024 12:42:12 +0000
parents 387d8c613b98
children 6a6175006cb9
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6:387d8c613b98 7:05f85f5bfc48
1 <tool id="gtdbtk_database_installer" name="GTDB-Tk Database Installer" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="gtdbtk_database_installer" name="GTDB-Tk Database Installer" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">202</token> 4 <token name="@TOOL_VERSION@">202</token>
5 <token name="@VERSION_SUFFIX@">2</token> 5 <token name="@VERSION_SUFFIX@">3</token>
6 <token name="@PROFILE@">20.09</token> 6 <token name="@PROFILE@">20.09</token>
7 </macros> 7 </macros>
8 <requirements> 8 <requirements>
9 <requirement type="package" version="3.10.2">python</requirement> 9 <requirement type="package" version="3.10.2">python</requirement>
10 </requirements> 10 </requirements>
11 <command> 11 <command>
12 <![CDATA[ 12 <![CDATA[
13 python '$__tool_directory__/gtdbtk_database_installer.py' 13 python '$__tool_directory__/gtdbtk_database_installer.py'
14 --database_name '$database_name' 14 --release '$release'
15 --release '$release' 15 --out_file '$out_file'
16 --out_file '$out_file' 16 $meta
17 $meta 17 $test
18 $test
19 ]]> 18 ]]>
20 </command> 19 </command>
21 <inputs> 20 <inputs>
22 <param name="database_name" type="text" value="" label="Database name or description" help="This value will be displayed in the GTDB-Tk Database select list"/> 21 <param name="meta" type="boolean" truevalue="--meta" falsevalue="" checked="false" label="Only store GTDBTK metadata in a dedicated data table. " />
23 <param name="meta" type="boolean" truevalue="--meta" falsevalue="" checked="false" label="Only store GTDBTK metadata in a dedicated data table. " /> 22 <param name="test" type="hidden" value="" checked="false" label="Run a dry test run!" />
24 <param name="test" type="hidden" value="" checked="false" label="Run a dry test run !" />
25 <param name="release" type="select" multiple="false" label="GTDB Release"> 23 <param name="release" type="select" multiple="false" label="GTDB Release">
26 <option value="202">202</option> 24 <option value="202">202</option>
27 <option value="207">207</option> 25 <option value="207">207</option>
28 <option value="214">214</option> 26 <option value="214">214</option>
29 <option value="220">220</option> 27 <option value="220">220</option>
32 <outputs> 30 <outputs>
33 <data name="out_file" format="data_manager_json"/> 31 <data name="out_file" format="data_manager_json"/>
34 </outputs> 32 </outputs>
35 <tests> 33 <tests>
36 <test> 34 <test>
37 <!-- TODO -->
38 <!-- Not actually installing a huge GTDB-Tk database --> 35 <!-- Not actually installing a huge GTDB-Tk database -->
39 <!-- but it will check if all urls exist --> 36 <!-- but it will check if all urls exist -->
40 <param name="release" value="202"/> 37 <param name="release" value="202"/>
41 <param name="database_name" value="GTDB-Tk database release 202"/>
42 <param name="test" value="--test"/> 38 <param name="test" value="--test"/>
43 <output name="out_file"> 39 <output name="out_file">
44 <assert_contents> 40 <assert_contents>
45 <has_text text="GTDB-Tk database release 202"/> 41 <has_text text="Full Database - release 202 "/>
46 <has_text text="release_202"/> 42 <has_text text="full_database_release_202_downloaded"/>
47 </assert_contents> 43 </assert_contents>
48 </output> 44 </output>
49 </test> 45 </test>
50 <test> 46 <test>
51 <!-- Test meta data download with tsv.gz--> 47 <!-- Test meta data download with tsv.gz-->
52 <param name="release" value="220"/> 48 <param name="release" value="220"/>
53 <param name="database_name" value="GTDB-Tk database release 220 metadata"/>
54 <param name="meta" value="true"/> 49 <param name="meta" value="true"/>
55 <output name="out_file"> 50 <output name="out_file">
56 <assert_contents> 51 <assert_contents>
57 <has_text text="GTDB-Tk database release 220 metadata"/> 52 <has_text text="Metadata Tables - release 220"/>
58 <has_text text="release_220"/> 53 <has_text text="metadata_tables_release_220_downloaded_"/>
59 </assert_contents> 54 </assert_contents>
60 </output> 55 </output>
61 </test> 56 </test>
62 <test> 57 <test>
63 <!-- Test meta data download with tar.gz --> 58 <!-- Test meta data download with tar.gz -->
64 <param name="release" value="207"/> 59 <param name="release" value="207"/>
65 <param name="database_name" value="GTDB-Tk database release 207 metadata"/>
66 <param name="meta" value="true"/> 60 <param name="meta" value="true"/>
67 <output name="out_file"> 61 <output name="out_file">
68 <assert_contents> 62 <assert_contents>
69 <has_text text="GTDB-Tk database release 207 metadata"/> 63 <has_text text="Metadata Tables - release 207"/>
70 <has_text text="release_207"/> 64 <has_text text="metadata_tables_release_207_downloaded_"/>
71 </assert_contents> 65 </assert_contents>
72 </output> 66 </output>
73 </test> 67 </test>
74 </tests> 68 </tests>
75 <help> 69 <help>