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changeset 8:ce135864629c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 9d2052269bfbca81a5f9cd10c3153e611358a329
author iuc
date Tue, 24 Oct 2017 07:27:53 -0400
parents 7adfd0589f49
children 68693743661e
files readme.rst snpEff.xml snpEff_macros.xml tool-data/snpeffv_annotations.loc.sample tool-data/snpeffv_databases.loc.sample tool_data_table_conf.xml.sample
diffstat 6 files changed, 5 insertions(+), 24 deletions(-) [+]
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line diff
--- a/readme.rst	Tue Apr 18 09:33:56 2017 -0400
+++ b/readme.rst	Tue Oct 24 07:27:53 2017 -0400
@@ -13,8 +13,8 @@
 
 There are 2 datamanagers to download and install prebuilt SnpEff genome databases:
 
-* data_manager_snpeff_databases: generates a list of available SnpEff genome databases into the ``tool-data/snpeff_databases.loc`` file
-* data_manager_snpeff_download: downloads a SnpEff genome database selected from ``tool-data/snpeff_databases.loc`` and adds entries to ``snpeff_genomedb.loc``, ``snpeff_regulationdb.loc`` and ``snpeff_annotations.loc``
+* data_manager_snpeff_databases: generates a list of available SnpEff genome databases into the ``tool-data/snpeffv_databases.loc`` file
+* data_manager_snpeff_download: downloads a SnpEff genome database selected from ``tool-data/snpeffv_databases.loc`` and adds entries to ``snpeffv_genomedb.loc`` and ``snpeffv_regulationdb.loc`` .
 
 SnpEff citation: |Cingolani2012program|_.
 
--- a/snpEff.xml	Tue Apr 18 09:33:56 2017 -0400
+++ b/snpEff.xml	Tue Oct 24 07:27:53 2017 -0400
@@ -218,7 +218,7 @@
             <option value="-noNextProt">Disable NextProt annotations</option>
             <option value="-noInteraction">Disable interaction annotations</option>
             <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
-            <!--  onlyReg option results in ifrequent exceptions with version 4.3k
+            <!--  onlyReg option results in frequent exceptions with version 4.3k
             <option value="-onlyReg">Only use regulation tracks</option>
             -->
         </param>
--- a/snpEff_macros.xml	Tue Apr 18 09:33:56 2017 -0400
+++ b/snpEff_macros.xml	Tue Oct 24 07:27:53 2017 -0400
@@ -1,7 +1,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="4.3k">snpeff</requirement>
+            <requirement type="package" version="4.3r">snpeff</requirement>
         </requirements>
     </xml>
   <xml name="stdio">
@@ -15,7 +15,7 @@
 snpEff -version
     ]]></version_command>
   </xml>
-  <token name="@WRAPPER_VERSION@">4.3k</token>
+  <token name="@WRAPPER_VERSION@">4.3r</token>
   <token name="@SNPEFF_VERSION@">SnpEff4.3</token>
   <token name="@SNPEFF_DATABASE_URL@">https://sourceforge.net/projects/snpeff/files/databases/v4_3/</token>
   <token name="@EXTERNAL_DOCUMENTATION@">
--- a/tool-data/snpeffv_annotations.loc.sample	Tue Apr 18 09:33:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-## Regulation Databases for SnpEff 
-## These are from the list on: http://snpeff.sourceforge.net/download.html
-#key	snpeff_version	genome	annotation_name description
-#SnpEff4.0_GRCh37.75	SnpEff4.0	GRCh37.75	nextprot	nextprot
-#SnpEff4.0_GRCh38.76	SnpEff4.1	GRCh38.76	motif	motif
--- a/tool-data/snpeffv_databases.loc.sample	Tue Apr 18 09:33:56 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-## Available Databases for SnpEff 
-## These are from the list on: http://snpeff.sourceforge.net/download.html
-## the Description field in this sample is "Genome : Version" 
-#key	snpeff_version	Version	Description
-#SnpEff4.0_GRCh37.75	SnpEff4.0	GRCh37.75	Homo sapiens : GRCh37.75
--- a/tool_data_table_conf.xml.sample	Tue Apr 18 09:33:56 2017 -0400
+++ b/tool_data_table_conf.xml.sample	Tue Oct 24 07:27:53 2017 -0400
@@ -7,13 +7,4 @@
         <columns>key, version, genome, value, name</columns>
         <file path="tool-data/snpeffv_regulationdb.loc" />
     </table>
-    <table name="snpeffv_annotations" comment_char="#" allow_duplicate_entries="False">
-        <columns>key, version, genome, value, name</columns>
-        <file path="tool-data/snpeffv_annotations.loc" />
-    </table>
-    <table name="snpeffv_databases" comment_char="#" allow_duplicate_entries="False">
-        <columns>key, version, value, name</columns>
-        <file path="tool-data/snpeffv_databases.loc" />
-    </table>
 </tables>
-