Mercurial > repos > iuc > data_manager_gemini_database_downloader

comparison data_manager/data_manager_gemini_download.xml @ 4:fe5a9a7d95b0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
author iuc
date Fri, 14 Dec 2018 12:40:15 -0500
parents 172815da3d41
children f57426daa04d
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3:172815da3d41 4:fe5a9a7d95b0
1 <tool id="data_manager_gemini_download" name="GEMINI Download" version="0.18.1" tool_type="manage_data"> 1 <tool id="data_manager_gemini_download" name="GEMINI Download" version="@VERSION@.1" tool_type="manage_data">
2 <description>Download a new database</description> 2 <description>the annotation files required by the GEMINI suite of tools</description>
3 <macros>
4 <token name="@VERSION@">0.18.1</token>
5 <token name="@DB_VERSION@">181</token>
6 </macros>
3 <requirements> 7 <requirements>
4 <requirement type="package" version="0.18.1">gemini</requirement> 8 <requirement type="package" version="@VERSION@">gemini</requirement>
5 </requirements> 9 </requirements>
6 <command detect_errors="exit_code"> 10 <command detect_errors="exit_code">
7 python '$__tool_directory__/data_manager_gemini_download.py' '$out_file' 11 python '$__tool_directory__/data_manager_gemini_download.py' '$out_file'
8 </command> 12 </command>
9 <inputs> 13 <inputs>
10 <param name="cadd" type="boolean" truevalue="--extra cadd_score" falsevalue="" checked="True" 14 <param name="cadd" type="boolean" truevalue="--extra cadd_score" falsevalue="" checked="True"
11 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)"/>
12 <param name="gerp_bp" type="boolean" truevalue="--extra gerp_bp" falsevalue="" checked="True" 16 <param name="gerp_bp" type="boolean" truevalue="--extra gerp_bp" falsevalue="" checked="True"
13 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@"/>
14 </inputs> 19 </inputs>
15 <outputs> 20 <outputs>
16 <data name="out_file" format="data_manager_json" label="${tool.name}"/> 21 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
17 </outputs> 22 </outputs>
18 <tests> 23 <tests>
19 </tests> 24 </tests>
20 <help> 25 <help>
21 This tool downloads the GEMINI databases. 26 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.
22 28
23 For details about this tool, please go to http://gemini.readthedocs.org 29 Please visit http://gemini.readthedocs.io for details about GEMINI.
30
31 .. _GERP: http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html
32 .. _CADD: https://cadd.gs.washington.edu/
24 </help> 33 </help>
25 <citations> 34 <citations>
26 <citation type="doi">10.1371/journal.pcbi.1003153</citation> 35 <citation type="doi">10.1371/journal.pcbi.1003153</citation>
27 </citations> 36 </citations>
28 </tool> 37 </tool>