Mercurial > repos > iuc > data_manager_snpeff

changeset 7:a6400027d849 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 9d2052269bfbca81a5f9cd10c3153e611358a329
author iuc
date Tue, 24 Oct 2017 07:27:38 -0400
parents 2107b4f40945
children d107d20dc6bd
files data_manager/data_manager_snpEff_databases.xml data_manager/data_manager_snpEff_download.py data_manager/data_manager_snpEff_download.xml data_manager_conf.xml tool-data/snpeffv_annotations.loc.sample tool_data_table_conf.xml.sample
diffstat 6 files changed, 6 insertions(+), 34 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_snpEff_databases.xml	Tue Apr 18 12:56:13 2017 -0400
+++ b/data_manager/data_manager_snpEff_databases.xml	Tue Oct 24 07:27:38 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.3k" tool_type="manage_data">
+<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.3r" tool_type="manage_data">
     <description>Read the list of available SnpEff databases</description>
     <requirements>
-        <requirement type="package" version="4.3k">snpeff</requirement>
+        <requirement type="package" version="4.3.1r">snpeff</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 python '$__tool_directory__/data_manager_snpEff_databases.py' '$out_file'
--- a/data_manager/data_manager_snpEff_download.py	Tue Apr 18 12:56:13 2017 -0400
+++ b/data_manager/data_manager_snpEff_download.py	Tue Oct 24 07:27:38 2017 -0400
@@ -93,8 +93,6 @@
         sys.exit( return_code )
     # search data_dir/genome_version for files
     regulation_pattern = 'regulation_(.+).bin'
-    #  annotation files that are included in SnpEff by a flag
-    annotations_dict = {'nextProt.bin': '-nextprot', 'motif.bin': '-motif', 'interactions.bin': '-interaction'}
     genome_path = os.path.join(data_dir, genome_version)
     snpeff_version = getSnpeffVersion()
     key = snpeff_version + '_' + genome_version
@@ -112,11 +110,6 @@
                         name = m.groups()[0]
                         data_table_entry = dict(key=key, version=snpeff_version, genome=genome_version, value=name, name=name)
                         _add_data_table_entry( data_manager_dict, 'snpeffv_regulationdb', data_table_entry )
-                    elif fname in annotations_dict:
-                        value = annotations_dict[fname]
-                        name = value.lstrip('-')
-                        data_table_entry = dict(key=key, version=snpeff_version, genome=genome_version, value=value, name=name)
-                        _add_data_table_entry( data_manager_dict, 'snpeffv_annotations', data_table_entry )
     return data_manager_dict
 
 
--- a/data_manager/data_manager_snpEff_download.xml	Tue Apr 18 12:56:13 2017 -0400
+++ b/data_manager/data_manager_snpEff_download.xml	Tue Oct 24 07:27:38 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.3k" tool_type="manage_data">
+<tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.3r" tool_type="manage_data">
     <description>Download a new database</description>
     <requirements>
-        <requirement type="package" version="4.3k">snpeff</requirement>
+        <requirement type="package" version="4.3.1r">snpeff</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 python '$__tool_directory__/data_manager_snpEff_download.py'
@@ -25,15 +25,14 @@
                     <!-- Check that a genome was added -->
                     <has_text text="GRCh38.76" />
                     <has_text text="snpeffv_regulationdb" />
-                    <has_text text="snpeffv_annotations" />
                 </assert_contents>
             </output>
         </test>
     </tests>
     <help><![CDATA[
-This tool downloads a SnpEff database and populates the data tables: snpeffv_genomedb, snpeffv_regulationdb, and snpeffv_annotations.
+This tool downloads a SnpEff database and populates the data tables: snpeffv_genomedb, snpeffv_regulationdb.
 
-To see the list of available SnpEff genomes run the "SnpEff Databases" data manager which records the available genome databases in data table: snpeff4_databases
+To see the list of available SnpEff genomes, run the "SnpEff Databases" data manager which records the available genome databases in data table: snpeffv_databases.
 
 The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/
 
--- a/data_manager_conf.xml	Tue Apr 18 12:56:13 2017 -0400
+++ b/data_manager_conf.xml	Tue Oct 24 07:27:38 2017 -0400
@@ -35,16 +35,5 @@
         <column name="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
       </output>
     </data_table>
-    <data_table name="snpeffv_annotations">  <!-- Defines a Data Table to be modified. -->
-      <output> <!-- Handle the output of the Data Manager Tool -->
-        <column name="key" /> <!-- columns that are going to be specified by the Data Manager Tool -->
-        <column name="version" /> <!-- columns that are going to be specified by the Data Manager Tool -->
-        <column name="genome" /> <!-- columns that are going to be specified by the Data Manager Tool -->
-        <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
-        <column name="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
-      </output>
-    </data_table>
   </data_manager>
 </data_managers>
-
-
--- a/tool-data/snpeffv_annotations.loc.sample	Tue Apr 18 12:56:13 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_table_conf.xml.sample	Tue Apr 18 12:56:13 2017 -0400
+++ b/tool_data_table_conf.xml.sample	Tue Oct 24 07:27:38 2017 -0400
@@ -7,10 +7,6 @@
         <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" />