Mercurial > repos > iuc > data_manager_gemini_database_downloader
view 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 |
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date | Sat, 03 Dec 2022 10:37:24 +0000 |
parents | f57426daa04d |
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<tool id="data_manager_gemini_download" name="GEMINI Download" version="@VERSION@+galaxy1" tool_type="manage_data" profile="18.09"> <description>the annotation files required by the GEMINI suite of tools</description> <macros> <token name="@VERSION@">0.20.1</token> <token name="@DB_VERSION@">200</token> </macros> <requirements> <requirement type="package" version="@VERSION@">gemini</requirement> </requirements> <command detect_errors="exit_code"> python '$__tool_directory__/data_manager_gemini_download.py' '$out_file' </command> <inputs> <param name="cadd" type="boolean" truevalue="cadd" falsevalue="" checked="True" label="Download CADD scores for GEMINI database annotation" help="(--extra cadd_score)"/> <param name="gerp_bp" type="boolean" truevalue="gerp_bp" falsevalue="" checked="True" label="Download GERP for GEMINI database annotation" help="(--extra gerp_bp)"/> <param name="gemini_db_version" type="hidden" value="@DB_VERSION@"/> <param name="test_data_manager" type="hidden" value=""/> </inputs> <outputs> <data name="out_file" format="data_manager_json" label="${tool.name}"/> </outputs> <tests> <test expect_num_outputs="1"> <param name="test_data_manager" value="--test" /> <param name="cadd" value="false" /> <param name="gerp_bp" value="false" /> <output name="out_file" file="test.json" compare="re_match" /> </test> <!-- Test 2 with the latest option --> <test expect_num_outputs="1"> <param name="test_data_manager" value="--test" /> <output name="out_file"> <assert_contents> <has_text text=""name": "GEMINI annotations w/ GERP & CADD" /> </assert_contents> </output> </test> </tests> <help> This tool downloads the GEMINI annotation files and makes them available to corresponding versions of the GEMINI suite of tools. Downloading the (very large) CADD_ scores and GERP_ annotation files is optional. Please visit http://gemini.readthedocs.io for details about GEMINI. .. _GERP: http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html .. _CADD: https://cadd.gs.washington.edu/ </help> <citations> <citation type="doi">10.1371/journal.pcbi.1003153</citation> </citations> </tool>