Mercurial > repos > jjohnson > data_manager_snpeff

changeset 4:6a378d0f4856

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Only download by name, available genome list now too large to be practical
author Jim Johnson <jj@umn.edu>
date Thu, 23 Oct 2014 05:43:46 -0500
parents c6769a700e55
children 78bcf4ac437c
files data_manager/data_manager_snpEff_databases.xml data_manager/data_manager_snpEff_download.xml data_manager_conf.xml repository_dependencies.xml
diffstat 4 files changed, 15 insertions(+), 33 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_snpEff_databases.xml	Tue Oct 21 14:04:33 2014 -0500
+++ b/data_manager/data_manager_snpEff_databases.xml	Thu Oct 23 05:43:46 2014 -0500
@@ -20,7 +20,7 @@
                 <output name="out_file">
                     <assert_contents>
                         <!-- Check that a genome was added -->
-                        <has_text text="GRCh37.72" />
+                        <has_text text="GRCh38.76" />
                     </assert_contents>
                 </output>
             </test>
--- a/data_manager/data_manager_snpEff_download.xml	Tue Oct 21 14:04:33 2014 -0500
+++ b/data_manager/data_manager_snpEff_download.xml	Thu Oct 23 05:43:46 2014 -0500
@@ -5,35 +5,13 @@
     </requirements>
     <command interpreter="python">
         data_manager_snpEff_download.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar --config \$SNPEFF_JAR_PATH/snpEff.config 
-        #if $snpDb.genomeSrc == "named":
-          --genome_version "${snpDb.genome_version}"
-        #else
-          --genome_version "${snpDb.genome_databases.fields.value}"
-          --organism "${snpDb.genome_databases.fields.name}"
-        #end if
-        "$out_file"
+          --genome_version "$genome_version" "$out_file"
         </command>
     <inputs>
-        <conditional name="snpDb">
-            <param name="genomeSrc" type="select" label="Select Genome Version">
-                <help>The list is very large and may take some time to display on your browser</help>
-                <option value="named">By Genome Version Name</option>
-                <option value="cached">Select from list</option>
-            </param>
-            <when value="named">
-                <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh37.74)">
-                    <help>http://sourceforge.net/projects/snpeff/files/databases/</help>
-                    <validator type="regex" message="A genome version name is required">\S+</validator>
-                </param>
-            </when>
-            <when value="cached">
-                <param name="genome_databases" type="select" display="checkboxes" multiple="true" label="Genome Version">
-                    <options from_data_table="snpeff4_databases">
-                        <filter type="sort_by" column="0" />
-                    </options>
-                </param>
-            </when>
-        </conditional>
+        <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
+            <help>http://sourceforge.net/projects/snpeff/files/databases/</help>
+            <validator type="regex" message="A genome version name is required">\S+</validator>
+        </param>
     </inputs>
 
     <outputs>
@@ -45,7 +23,6 @@
     </stdio>
     <tests>
         <test>
-            <param name="genomeSrc"  value="named"/>
             <param name="genome_version" value="GRCh38.76"/>
             <output name="out_file">
                 <assert_contents>
@@ -59,7 +36,12 @@
     </tests>
     <help>
 
-This tool downloads a SnpEff database.
+This tool downloads a SnpEff database and populates data tables: snpeff4_genomedb, snpeff4_regulationdb, and snpeff4_annotations.
+
+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 
+
+The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/
+
 
 For details about this tool, please go to http://snpEff.sourceforge.net
 
--- a/data_manager_conf.xml	Tue Oct 21 14:04:33 2014 -0500
+++ b/data_manager_conf.xml	Thu Oct 23 05:43:46 2014 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <data_managers>
-  <data_manager tool_file="data_manager/data_manager_snpEff_databases.xml" id="data_manager_snpeff_databases" >
+  <data_manager tool_file="data_manager/data_manager_snpEff_databases.xml" id="data_manager_snpeff4_databases" >
     <data_table name="snpeff4_databases">  <!-- Defines a Data Table to be modified. -->
       <output> <!-- Handle the output of the Data Manager Tool -->
         <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
@@ -8,7 +8,7 @@
       </output>
     </data_table>
   </data_manager>
-  <data_manager tool_file="data_manager/data_manager_snpEff_download.xml" id="data_manager_snpeff_download" >
+  <data_manager tool_file="data_manager/data_manager_snpEff_download.xml" id="data_manager_snpeff4_download" >
     <data_table name="snpeff4_genomedb">  <!-- Defines a Data Table to be modified. -->
       <output> <!-- Handle the output of the Data Manager Tool -->
         <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
--- a/repository_dependencies.xml	Tue Oct 21 14:04:33 2014 -0500
+++ b/repository_dependencies.xml	Thu Oct 23 05:43:46 2014 -0500
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="This requires the SnpEff datatype definitions.">
-    <repository name="snpeff_datatypes" owner="jjohnson" changeset_revision="cd8f8c54bf9a" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+    <repository name="snpeff_datatypes" owner="jjohnson" changeset_revision="b33911fdbac4" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
 </repositories>