Mercurial > repos > iuc > data_manager_gemini_database_downloader

comparison data_manager/data_manager_gemini_download.xml @ 9:27a6a256cd23 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 275b7863ff4f8b0dff9cd7ea6c4b635694f0168d
author iuc
date Sat, 03 Dec 2022 10:37:24 +0000
parents f57426daa04d
children
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8:52b6a4d98009 9:27a6a256cd23
1 <tool id="data_manager_gemini_download" name="GEMINI Download" version="@VERSION@" tool_type="manage_data"> 1 <tool id="data_manager_gemini_download" name="GEMINI Download" version="@VERSION@+galaxy1" tool_type="manage_data" profile="18.09">
2 <description>the annotation files required by the GEMINI suite of tools</description> 2 <description>the annotation files required by the GEMINI suite of tools</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">0.20.1</token> 4 <token name="@VERSION@">0.20.1</token>
5 <token name="@DB_VERSION@">200</token> 5 <token name="@DB_VERSION@">200</token>
6 </macros> 6 </macros>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"> 10 <command detect_errors="exit_code">
11 python '$__tool_directory__/data_manager_gemini_download.py' '$out_file' 11 python '$__tool_directory__/data_manager_gemini_download.py' '$out_file'
12 </command> 12 </command>
13 <inputs> 13 <inputs>
14 <param name="cadd" type="boolean" truevalue="--extra cadd_score" falsevalue="" checked="True" 14 <param name="cadd" type="boolean" truevalue="cadd" falsevalue="" checked="True"
15 label="Download CADD scores for GEMINI database annotation" help="(--extra cadd_score)"/> 15 label="Download CADD scores for GEMINI database annotation" help="(--extra cadd_score)"/>
16 <param name="gerp_bp" type="boolean" truevalue="--extra gerp_bp" falsevalue="" checked="True" 16 <param name="gerp_bp" type="boolean" truevalue="gerp_bp" falsevalue="" checked="True"
17 label="Download GERP for GEMINI database annotation" help="(--extra gerp_bp)"/> 17 label="Download GERP for GEMINI database annotation" help="(--extra gerp_bp)"/>
18 <param name="gemini_db_version" type="hidden" value="@DB_VERSION@"/> 18 <param name="gemini_db_version" type="hidden" value="@DB_VERSION@"/>
19 <param name="test_data_manager" type="hidden" value=""/>
19 </inputs> 20 </inputs>
20 <outputs> 21 <outputs>
21 <data name="out_file" format="data_manager_json" label="${tool.name}"/> 22 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
22 </outputs> 23 </outputs>
23 <tests> 24 <tests>
25 <test expect_num_outputs="1">
26 <param name="test_data_manager" value="--test" />
27 <param name="cadd" value="false" />
28 <param name="gerp_bp" value="false" />
29 <output name="out_file" file="test.json" compare="re_match" />
30 </test>
31 <!-- Test 2 with the latest option -->
32 <test expect_num_outputs="1">
33 <param name="test_data_manager" value="--test" />
34 <output name="out_file">
35 <assert_contents>
36 <has_text text="&quot;name&quot;: &quot;GEMINI annotations w/ GERP &amp; CADD" />
37 </assert_contents>
38 </output>
39 </test>
24 </tests> 40 </tests>
25 <help> 41 <help>
26 This tool downloads the GEMINI annotation files and makes them available to 42 This tool downloads the GEMINI annotation files and makes them available to
27 corresponding versions of the GEMINI suite of tools. Downloading the (very large) CADD_ scores and GERP_ annotation files is optional. 43 corresponding versions of the GEMINI suite of tools. Downloading the (very large) CADD_ scores and GERP_ annotation files is optional.
28 44