Mercurial > repos > iuc > data_manager_gemini_database_downloader

diff 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
line wrap: on
line diff
--- a/data_manager/data_manager_gemini_download.xml	Tue Apr 04 18:09:05 2017 -0400
+++ b/data_manager/data_manager_gemini_download.xml	Fri Dec 14 12:40:15 2018 -0500
@@ -1,7 +1,11 @@
-<tool id="data_manager_gemini_download" name="GEMINI Download" version="0.18.1" tool_type="manage_data">
-    <description>Download a new database</description>
+<tool id="data_manager_gemini_download" name="GEMINI Download" version="@VERSION@.1" tool_type="manage_data">
+    <description>the annotation files required by the GEMINI suite of tools</description>
+    <macros>
+        <token name="@VERSION@">0.18.1</token>
+        <token name="@DB_VERSION@">181</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="0.18.1">gemini</requirement>
+        <requirement type="package" version="@VERSION@">gemini</requirement>
     </requirements>
     <command detect_errors="exit_code">
         python '$__tool_directory__/data_manager_gemini_download.py' '$out_file'
@@ -11,6 +15,7 @@
             label="Download CADD scores for GEMINI database annotation" help="(--extra cadd_score)"/>
         <param name="gerp_bp" type="boolean" truevalue="--extra 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@"/>
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json" label="${tool.name}"/>
@@ -18,9 +23,13 @@
     <tests>
     </tests>
     <help>
-This tool downloads the GEMINI databases.
+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.
 
-For details about this tool, please go to http://gemini.readthedocs.org
+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>