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comparison data_manager/data_manager_semibin.xml @ 1:d584aacd7d13 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
author iuc
date Fri, 01 Aug 2025 21:25:02 +0000
parents 676915c44e1e
children
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0:676915c44e1e 1:d584aacd7d13
1 <tool id="data_manager_semibin" name="Download reference genomes (GTDB) for SemiBin" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="data_manager_semibin" name="Download reference genomes (GTDB) for SemiBin" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description></description> 2 <description></description>
3 <macros>
4 <token name="@TOOL_VERSION@">2.0.2</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 <token name="@PROFILE@">24.0</token>
7 </macros>
3 <requirements> 8 <requirements>
4 <requirement type="package" version="@TOOL_VERSION@">semibin</requirement> 9 <requirement type="package" version="@TOOL_VERSION@">semibin</requirement>
5 </requirements> 10 </requirements>
6 <macros>
7 <token name="@TOOL_VERSION@">1.1.1</token>
8 <token name="@VERSION_SUFFIX@">0</token>
9 <token name="@PROFILE@">21.01</token>
10 </macros>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 python '$__tool_directory__/data_manager_semibin.py' 12 mkdir -p '${out_file.extra_files_path}' &&
13 --json '$out_file' 13 #if $type == "test"
14 $type 14 touch '${out_file.extra_files_path}'/empty
15 #else
16 SemiBin download_GTDB --reference-db-data-dir '${out_file.extra_files_path}'
17 #end if
18 && cp '$dmjson' '$out_file'
15 ]]></command> 19 ]]></command>
20 <configfiles>
21 <configfile name="dmjson"><![CDATA[#slurp
22 #from datetime import datetime
23 #set value=datetime.now().strftime("%d%m%Y")
24 {
25 "data_tables":{
26 "gtdb":[
27 {
28 "value": "$value",
29 #if $type == "test"
30 "name": "Test",
31 "dbkey": "test",
32 #else
33 "name": "GTDB reference genome generated by MMseqs2 used in SemiBin",
34 "dbkey": "gtdb",
35 #end if
36 "path": "$out_file.extra_files_path"
37 }
38 ]
39 }
40 }
41 ]]></configfile>
42 </configfiles>
16 <inputs> 43 <inputs>
17 <param name="type" type="hidden" value="" /> 44 <param name="type" type="hidden" value="" />
18 </inputs> 45 </inputs>
19 <outputs> 46 <outputs>
20 <data name="out_file" format="data_manager_json"/> 47 <data name="out_file" format="data_manager_json"/>
21 </outputs> 48 </outputs>
22 <tests> 49 <tests>
23 <test expect_num_outputs="1"> 50 <test expect_num_outputs="1">
24 <param name="type" value="--test" /> 51 <param name="type" value="test" />
25 <output name="out_file"> 52 <output name="out_file">
26 <assert_contents> 53 <assert_contents>
27 <has_text text="test"/> 54 <has_text text="test"/>
28 <has_text text="Test"/> 55 <has_text text="Test"/>
29 </assert_contents> 56 </assert_contents>