# HG changeset patch
# User bgruening
# Date 1385735345 18000
# Node ID aecbd887892313fb10159e70f493e8abd3b05a2f
# Parent  0ad9733e22a43a7889eda29528b0c4bf33333183
Uploaded

diff -r 0ad9733e22a4 -r aecbd8878923 README
--- a/README	Fri Nov 29 09:27:22 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-These are galaxy tools for SnpEff a variant annotation and effect prediction tool by Pablo Cingolani. 
-It annotates and predicts the effects of variants on genes (such as amino acid changes).
-( http://snpeff.sourceforge.net/ )
-
-This repository contains a tool_dependencies.xml file that will attempt to automatically install SnpEff and SnpSift.   
-
-This will use the default location for genome reference downloads from the snpEff.config:
-data_dir = ~/snpEff/data/
-You can manually edit the installed snpEff.config and change the location, or you can create a symbolic link to the desired data location from ~/snpEff.
-
-The genome reference options used by the tools:
-    "SnpEff"  snpEff.xml
-    "SnpEff Download" snpEff_download.xml
-are taken from: tool-data/snpeffect_genomedb.loc
-
-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 
-  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,snpeff_annotations.loc 
-
-SnpEff citation:
-"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
-
-SnpSift citation:
-"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.
diff -r 0ad9733e22a4 -r aecbd8878923 readme.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Fri Nov 29 09:29:05 2013 -0500
@@ -0,0 +1,24 @@
+These are galaxy tools for SnpEff a variant annotation and effect prediction tool by Pablo Cingolani. 
+It annotates and predicts the effects of variants on genes (such as amino acid changes).
+( http://snpeff.sourceforge.net/ )
+
+This repository contains a tool_dependencies.xml file that will attempt to automatically install SnpEff and SnpSift.   
+
+This will use the default location for genome reference downloads from the snpEff.config:
+data_dir = ~/snpEff/data/
+You can manually edit the installed snpEff.config and change the location, or you can create a symbolic link to the desired data location from ~/snpEff.
+
+The genome reference options used by the tools:
+    "SnpEff"  snpEff.xml
+    "SnpEff Download" snpEff_download.xml
+are taken from: tool-data/snpeffect_genomedb.loc
+
+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 
+  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,snpeff_annotations.loc 
+
+SnpEff citation:
+"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
+
+SnpSift citation:
+"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.
diff -r 0ad9733e22a4 -r aecbd8878923 snpEff_macros.xml
--- a/snpEff_macros.xml	Fri Nov 29 09:27:22 2013 -0500
+++ b/snpEff_macros.xml	Fri Nov 29 09:29:05 2013 -0500
@@ -5,20 +5,6 @@
         </requirements>
     </xml>
   <xml name="stdio">
-    <conditional name="analysis_param_type">
-      <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
-        <option value="basic" selected="True">Basic</option>
-        <option value="advanced">Advanced</option>
-      </param>
-      <when value="basic">
-        <!-- Do nothing here -->
-      </when>
-      <when value="advanced">
-        <yield />
-      </when>
-    </conditional>
-  </xml>
-  <xml name="reference_source_selector_param">
     <stdio>
         <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />
         <exit_code range="1:"  level="fatal" description="Error" />