Mercurial > repos > iuc > data_manager_gemini_database_downloader
comparison data_manager/data_manager_gemini_download.xml @ 9:27a6a256cd23 draft default tip
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 |
comparison
equal
deleted
inserted
replaced
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=""name": "GEMINI annotations w/ GERP & 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 |