diff snpEff_download.xml @ 11:c5288d5a446e

Update to version 3.6 and refactor to new repositories: snpsift, snpeff_datatypes, data_manager_snpeff

--- a/snpEff_download.xml	Tue Dec 10 14:28:37 2013 -0600
+++ b/snpEff_download.xml	Thu Jun 26 08:40:30 2014 -0500
@@ -1,23 +1,53 @@
-<tool id="snpEff_download" name="SnpEff Download" version="3.4">
+<tool id="snpEff_download" name="SnpEff Download" version="3.6">
     <description>Download a new database</description>
     <expand macro="requirements" />
     <macros>
         <import>snpEff_macros.xml</import>
     </macros>
     <command>
-    echo $genomeVersion > $snpeff_db; 
-    java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.extra_files_path -v $genomeVersion > $logfile 
+    #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 > $logfile 
     </command>
     <inputs>
-        <param name="genomeVersion" type="select" label="Select the genome version you want to download">
-            <options from_data_table="snpeff_databases">
-                <filter type="sort_by" column="0" />
-            </options>
-        </param>
+        <conditional name="snpDb">
+            <param name="genomeSrc" type="select" label="Genome List">
+                <option value="named">By Name</option>
+                <option value="cached">Select from list</option>
+            </param>
+            <when value="named">
+                <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh37.74)">
+                <help>http://sourceforge.net/projects/snpeff/files/databases/</help>
+                <validator type="regex" message="A genome version name is required">\S+</validator>
+                </param>
+            </when>
+            <when value="cached">
+                <param name="genome_databases" type="select" display="checkboxes" multiple="true" label="Genome Version">
+                    <options from_data_table="snpeff_databases">
+                        <filter type="sort_by" column="0" />
+                    </options>
+                </param>
+            </when>
+        </conditional>
     </inputs>
     <outputs>
         <data format="txt" name="logfile" />
-        <data format="snpeffdb" name="snpeff_db" label="${genomeVersion}" />
+        <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>
     </outputs>
     <expand macro="stdio" />
     <help>