Mercurial > repos > iuc > data_manager_interproscan

comparison data_manager/interproscan.xml @ 0:3e344aedb267 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
author iuc
date Mon, 15 Nov 2021 17:20:14 +0000
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children d9a238ff2bc3
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-1:000000000000 0:3e344aedb267
1 <tool id="data_manager_interproscan" name="InterProScan data manager" version="0.0.1" tool_type="manage_data" profile="20.01">
2 <requirements>
3 <requirement type="package" version="5.52-86.0">interproscan</requirement>
4 <requirement type="package" version="2.26.0">requests</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 python '$__tool_directory__/interproscan.py'
8 $partial_data
9 --version '$version'
10 'interproscan'
11 '${output_file}'
12 ]]></command>
13 <inputs>
14 <param name="partial_data" type="hidden" value="" help="Used for testing"/>
15 <param name="version" type="text" value="" label="Version to download" help="Leave empty to download the latest version">
16 <validator type="regex" message="Version must be a valid InterProScan version (e.g. 5.52-86.0)">^([0-9]+\.[0-9]+-[0-9]+\.[0-9]+)?$</validator>
17 </param>
18 </inputs>
19 <outputs>
20 <data name="output_file" format="data_manager_json"/>
21 </outputs>
22 <tests>
23 <test>
24 <param name="partial_data" value="--partial"/>
25 <output name="output_file">
26 <assert_contents>
27 <has_text text="InterProScan 5."/>
28 <has_text text='"interproscan_version": "5.'/>
29 </assert_contents>
30 </output>
31 <assert_stdout>
32 <has_text text="Pressed and indexed" />
33 <has_text text="Completed indexing the hmm models" />
34 </assert_stdout>
35 </test>
36 <test>
37 <param name="partial_data" value="--partial"/>
38 <param name="version" value="5.51-85.0"/>
39 <output name="output_file">
40 <assert_contents>
41 <has_text text="InterProScan 5.51-85.0"/>
42 <has_text text='"interproscan_version": "5.51-85.0'/>
43 </assert_contents>
44 </output>
45 <assert_stdout>
46 <has_text text="Pressed and indexed" />
47 <has_text text="Completed indexing the hmm models" />
48 </assert_stdout>
49 </test>
50 <test expect_failure="true">
51 <param name="partial_data" value="--partial"/>
52 <param name="version" value="xxxx"/>
53 <assert_stderr>
54 <has_text text="Version must be a valid InterProScan version" />
55 </assert_stderr>
56 </test>
57 </tests>
58 <help><![CDATA[
59 This data managers fetches data from EBI FTP server for the InterProScan
60 annotation tool and updates the InterProScan data table.
61 ]]></help>
62 <citations>
63 <citation type="doi">10.1093/bioinformatics/btu031</citation>
64 <citation type="doi">10.7717/peerj.167</citation>
65 <citation type="doi">10.1093/bioinformatics/17.9.847</citation>
66 <citation type="doi">10.1093/nar/gki442</citation>
67 <citation type="doi">10.1093/nar/gkn785</citation>
68 </citations>
69 </tool>