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comparison data_manager/data_manager_deeparg.xml @ 0:4a72de3780aa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_deeparg commit 068be9bb0973bc877457d13d0d5a7c26a6cc1f96
author iuc
date Fri, 07 Feb 2025 12:17:25 +0000
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children 50f4ff01d845
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-1:000000000000 0:4a72de3780aa
1 <tool id="data_manager_deeparg" name="Download data for DeepARG" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="22.05">
2 <description></description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.0.4</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">deeparg</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 mkdir -p '$out_file.extra_files_path' &&
12 deeparg download_data -o '$out_file.extra_files_path/' &&
13 cp '$dmjson' '$out_file'
14 ]]></command>
15 <configfiles>
16 <configfile name="dmjson"><![CDATA[
17 #from datetime import date
18 {
19 "data_tables":{
20 "deeparg":[
21 {
22 "value": "deeparg_$version-#echo date.today().strftime('%d%m%Y')#",
23 "name": "Files needed for running deepARG v-$version-#echo date.today().strftime('%d%m%Y')#",
24 "path": "deeparg_$version",
25 "db_version": "$version"
26 }
27 ]
28 }
29 }]]>
30 </configfile>
31 </configfiles>
32 <inputs>
33 <param name="version" type="select" label="DB version">
34 <option value="@TOOL_VERSION@" selected="true">DeepARG version</option>
35 </param>
36 </inputs>
37 <outputs>
38 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
39 </outputs>
40 <tests>
41 <test expect_num_outputs="1">
42 <param name="version" value="1.0.4"/>
43 <output name="out_file">
44 <assert_contents>
45 <has_text text='"deeparg":'/>
46 <has_text text='"db_version": "1.0.4"'/>
47 <has_text_matching expression='"value": "deeparg_1.0.4-[0-9]{8}"'/>
48 <has_text_matching expression='"name": "Files needed for running deepARG v-1.0.4-[0-9]{8}"'/>
49 <has_text text='"path": "deeparg_1.0.4"'/>
50 </assert_contents>
51 </output>
52 </test>
53 </tests>
54 <help><![CDATA[
55 Download data necessary for running DeepARG. It is composed of the database, scripts, metadata and models files.
56 ]]></help>
57 <citations>
58 <citation type="doi">10.1186/s40168-018-0401-z</citation>
59 </citations>
60 </tool>