# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1414058966 18000
# Node ID 3790e16a0be0a450db351225b73284a9a9c9b38e
# Parent  fac49d7ea7d4355bd183d8de3d34c888de202be8
Add datatype: snpeffdbv4

diff -r fac49d7ea7d4 -r 3790e16a0be0 repository_dependencies.xml
--- a/repository_dependencies.xml	Tue Oct 21 14:40:44 2014 -0500
+++ b/repository_dependencies.xml	Thu Oct 23 05:09:26 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>
diff -r fac49d7ea7d4 -r 3790e16a0be0 snpEff.xml
--- a/snpEff.xml	Tue Oct 21 14:40:44 2014 -0500
+++ b/snpEff.xml	Thu Oct 23 05:09:26 2014 -0500
@@ -34,13 +34,13 @@
         #if $statsFile:
           -stats $statsFile 
         #end if
-        #if $offset.__str__ != '':
+        #if $offset.__str__ != 'default':
           ${offset} 
         #end if
         #if $chr.__str__.strip() != '':
           -chr "$chr" 
         #end if
-        $noLog 
+          $noLog 
         #if $snpDb.genomeSrc == 'cached':
           -dataDir ${snpDb.genomeVersion.fields.path}
           #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
@@ -114,7 +114,7 @@
                 </param>
             </when>
             <when value="history">
-                <param format="snpeffdb" name="snpeff_db" type="data" label="SnpEff Genome Version Data"/>
+                <param format="snpeffdbv4" name="snpeff_db" type="data" label="SnpEff Genome Version Data"/>
                 <!-- From metadata -->
                 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations">
                     <help>These are available for only a few genomes</help>
@@ -130,7 +130,10 @@
                 </param>
             </when>
             <when value="named">
-                <param name="genome_version" type="text" value="GRCh38.76" label="Snpff Version Name"/>
+                <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/v4_0/</help>
+                    <validator type="regex" message="A genome version name is required">\S+</validator>
+                </param>
             </when>
         </conditional>
 
@@ -194,7 +197,7 @@
         </param>
 
         <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
-            <option value="" selected="true">Use default (based on input type)</option>
+            <option value="default" selected="true">Use default (based on input type)</option>
             <option value="-0">Force zero-based positions (both input and output)</option>
             <option value="-1">Force one-based positions (both input and output)</option>
         </param>
diff -r fac49d7ea7d4 -r 3790e16a0be0 snpEff_databases.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff_databases.xml	Thu Oct 23 05:09:26 2014 -0500
@@ -0,0 +1,24 @@
+<tool id="snpEff_databases" name="SnpEff Available Databases" version="4.0.0">
+    <description></description>
+    <expand macro="requirements" />
+    <macros>
+        <import>snpEff_macros.xml</import>
+    </macros>
+    <command>
+    java -jar \$SNPEFF_JAR_PATH/snpEff.jar databases |  grep -v '^---' | sed 's/^Genome/#Genome/' | sed  's/  *//g' > $snpeff_dbs 
+    </command>
+    <inputs>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="snpeff_dbs" label="${tool.name} available databases" />
+    </outputs>
+    <expand macro="stdio" />
+    <help>
+
+@EXTERNAL_DOCUMENTATION@
+
+@CITATION_SECTION@
+
+    </help>
+</tool>
+
diff -r fac49d7ea7d4 -r 3790e16a0be0 snpEff_download.xml
--- a/snpEff_download.xml	Tue Oct 21 14:40:44 2014 -0500
+++ b/snpEff_download.xml	Thu Oct 23 05:09:26 2014 -0500
@@ -5,49 +5,17 @@
         <import>snpEff_macros.xml</import>
     </macros>
     <command>
-    #if $snpDb.genomeSrc == "named":
-      #set genomeVersion = $snpDb.genome_version
-      #set data_dir = $snpeff_db_named.extra_files_path
-    ## echo $snpDb.genome_version > $snpeff_db_named; 
-    ## java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db_named.extra_files_path -v $snpDb.genome_version > $logfile 
-    #else
-      #set genomeVersion = $snpDb.genome_databases.fields.value
-      #set data_dir = $snpeff_db_cached.extra_files_path
-    ## echo $snpeff_db_cached.extra_files_path > $snpeff_db_cached; 
-    ## java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db_cached.extra_files_path -v $snpeff_db_cached.extra_files_path > $logfile 
-    #end if
-    ## echo $genomeVersion > $snpeff_db; 
-    java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $data_dir -v $genomeVersion > $logfile 
+    java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.extra_files_path -v $genome_version > $logfile 
     </command>
     <inputs>
-        <conditional name="snpDb">
-            <param name="genomeSrc" type="select" label="Genome List">
-                <option value="named">By Name</option>
-                <option value="cached">Select from list</option>
-            </param>
-            <when value="named">
-                <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh37.74)">
-                <help>http://sourceforge.net/projects/snpeff/files/databases/</help>
-                <validator type="regex" message="A genome version name is required">\S+</validator>
-                </param>
-            </when>
-            <when value="cached">
-                <param name="genome_databases" type="select" display="checkboxes" multiple="true" label="Genome Version">
-                    <options from_data_table="snpeff4_databases">
-                        <filter type="sort_by" column="0" />
-                    </options>
-                </param>
-            </when>
-        </conditional>
+        <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh37.74)">
+            <help>http://sourceforge.net/projects/snpeff/files/databases/</help>
+            <validator type="regex" message="A genome version name is required">\S+</validator>
+        </param>
     </inputs>
     <outputs>
         <data format="txt" name="logfile" />
-        <data format="snpeffdb" name="snpeff_db_named" label="${tool.name} ${snpDb.genome_version}" >
-            <filter>snpDb['genomeSrc'] == "named"</filter>
-        </data>
-        <data format="snpeffdb" name="snpeff_db_cached" label="${tool.name} ${snpDb.genome_databases.fields.value}">
-            <filter>snpDb['genomeSrc'] == "cached"</filter>
-        </data>
+        <data format="snpeffdbv4" name="snpeff_db" label="${tool.name} ${genome_version}" />
     </outputs>
     <expand macro="stdio" />
     <help>