Mercurial > repos > sh477 > data_manager_vep_cache_downloader

changeset 8:3f3246b8972e draft default tip

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Uploaded
author sh477
date Tue, 05 Apr 2022 18:10:59 +0000
parents 7890790d2afd
children
files data_manager/data_manager_vep_cache_download.xml
diffstat 1 files changed, 36 insertions(+), 31 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_vep_cache_download.xml	Tue Mar 01 18:12:26 2022 +0000
+++ b/data_manager/data_manager_vep_cache_download.xml	Tue Apr 05 18:10:59 2022 +0000
@@ -1,31 +1,36 @@
 <tool id="data_manager_vep_cache_download" name="Download and install VEP cache" version="0.1" tool_type="manage_data">
-    <description>versioned annotation files for VEP</description>
-    <requirements>
-        <requirement type="package" version="3.9">python</requirement>
-    </requirements>
-    <command detect_errors="exit_code">
-        python '$__tool_directory__/data_manager_vep_cache_download.py' '$out_file'
-    </command>
-    <inputs>
-        <param name="dbkey" type="genomebuild"
-            label="DBKEY of genome that the VEP cache data is for"
-            help="" />
-        <param name="url" type="text" value="http://ftp.ensembl.org/pub/release-105/variation/indexed_vep_cache/"
-            label="FTP root url for VEP cache files" help="Release number should be equal to desired VEP version"/>
-        <param name="file_name" type="text" label="File name of cache file to be downloaded from root url" help="E.g. homo_sapiens_vep_105_GRCh38.tar.gz"/>
-    </inputs>
-    <outputs>
-        <data name="out_file" format="data_manager_json"/>
-    </outputs>
-    <tests>
-    <test>
-        <param name="dbkey" value="ci3"/>
-        <param name="url" value="http://ftp.ensembl.org/pub/release-105/variation/indexed_vep_cache/"/>
-        <param name="file_name" value="ciona_intestinalis_refseq_vep_105_KH.tar.gz"/>
-        <output name="out_file" file="from_test-meta.data_manager.json"/>
-        </test>
-    </tests>
-    <help>
+	<description>versioned annotation files for VEP</description>
+	<macros>
+		<token name="@VERSION@">105</token>
+	</macros>
+	<requirements>
+		<requirement type="package" version="@VERSION@.0">ensembl-vep</requirement>
+		<requirement type="package" version="3.6">python</requirement>
+	</requirements>
+	<command detect_errors="exit_code"><![CDATA[
+		python '$__tool_directory__/data_manager_vep_cache_download.py' '$out_file' &&
+		vep_convert_cache -r -d '${out_file.extra_files_path}' -s all -v all
+	]]></command>
+	<inputs>
+		<param name="dbkey" type="genomebuild"
+			label="DBKEY of genome that the VEP cache data is for"
+			help="" />
+		<param name="url" type="text" value="http://ftp.ensembl.org/pub/release-@VERSION@/variation/indexed_vep_cache/"
+			label="FTP root url for VEP cache files" help="Release number should be equal to desired VEP version"/>
+		<param name="file_name" type="text" label="File name of cache file to be downloaded from root url" help="E.g. homo_sapiens_vep_@VERSION@_GRCh38.tar.gz"/>
+	</inputs>
+	<outputs>
+		<data name="out_file" format="data_manager_json"/>
+	</outputs>
+	<tests>
+	<test>
+		<param name="dbkey" value="ci3"/>
+		<param name="url" value="http://ftp.ensembl.org/pub/release-@VERSION@/variation/indexed_vep_cache/"/>
+		<param name="file_name" value="ciona_intestinalis_refseq_vep_@VERSION@_KH.tar.gz"/>
+		<output name="out_file" file="from_test-meta.data_manager.json"/>
+		</test>
+	</tests>
+	<help>
 This tool downloads given versions of VEP cache annotation files and makes them available to Ensembl VEP in Galaxy via the
 "vep_versioned_annotation_cache" data table. You should use the indexed version of the cache files and it is strongly 
 recommended to use the cache files which version number matches the VEP version number. Note that for most genomes there 
@@ -34,8 +39,8 @@
 
 A general introduction to the VEP cache and download links can be found on the official website:
 https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html
-    </help>
-    <citations>
-        <citation type="doi">10.1186/s13059-016-0974-4</citation>
-    </citations>
+	</help>
+	<citations>
+		<citation type="doi">10.1186/s13059-016-0974-4</citation>
+	</citations>
 </tool>
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