# HG changeset patch
# User iuc
# Date 1428633428 14400
# Node ID 84e33833420ddc457d9f3ee1e5c75775da08a145
# Parent  206675156f0c75f8f1cdc4599093385c0712c4fe
Uploaded

diff -r 206675156f0c -r 84e33833420d snpSift_dbnsfp.xml
--- a/snpSift_dbnsfp.xml	Wed Apr 08 22:47:01 2015 -0400
+++ b/snpSift_dbnsfp.xml	Thu Apr 09 22:37:08 2015 -0400
@@ -1,5 +1,5 @@
-<tool id="snpSift_dbnsfp_generic" name="SnpSift dbNSFP" version="4.0.0">
-    <description>Add Annotations from dbNSFP and similar annotation DBs</description>
+<tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="4.0.0">
+    <description>Add Annotations from dbNSFP</description>
     <expand macro="requirements" />
     <macros>
         <import>snpSift_macros.xml</import>
@@ -30,8 +30,8 @@
             <when value="cached">
                 <param name="dbnsfp" type="select" label="Genome">
                     <options from_data_table="snpsift_dbnsfp">
-                        <column name="name" index="2"/>
-                        <column name="value" index="3"/>
+                        <column name="name" index="1"/>
+                        <column name="value" index="2"/>
                     </options>
                 </param>
                 <param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with">
@@ -73,7 +73,6 @@
     <help>
 
 The dbNSFP is an integrated database of functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.).
-It contains variant annotations such as:
 
 
   1000Gp1_AC
@@ -242,47 +241,32 @@
     rs numbers from UniSNP, which is a cleaned version of dbSNP build 129, in format: rs number1;rs number2;...
 
 
-
-The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp is in the SnpSift documentation:
-http://snpeff.sourceforge.net/SnpSift.html#dbNSFP
+The website for  dbNSFP database is https://sites.google.com/site/jpopgen/dbNSFP  and there is only annotation for human hg18 and hg19 genome builds. 
 
-A couple dbNSFP databases are prebuilt for SnpSift at: 
-http://sourceforge.net/projects/snpeff/files/databases/dbNSFP/
-
-
-
-
-**Uploading Your Own Annotations for any Genome**
+However, any dbNSFP-like tabular file that be can used with SnpSift dbnsfp if it has::
 
-The website for dbNSFP databases releases is:  
-https://sites.google.com/site/jpopgen/dbNSFP
-
-But there is only annotation for human hg18, hg19,  and hg38 genome builds. 
-
-However, any dbNSFP-like tabular file that be can used with SnpSift dbnsfp if it has:
-
-  - The first line of the file must be column headers that name the annotations.  
-  - The first 4 columns are required and must be:
-
-    1. #chr		- chromosome 
-    2. pos(1-coor)	- position in chromosome
-    3. ref		- reference base
-    4. alt		- alternate base
-
+	- The first line of the file must be column headers that name the annotations.  
+	- The first 4 columns are required and must be::
+		1. chromosome 
+		2. position in chromosome
+		3. reference base
+		4. alternate base
 
 For example:
 
 ::
 
 	#chr	pos(1-coor)	ref	alt	aaref	aaalt	genename	SIFT_score
-	  4	 100239319	 T	 A	  H	  L	 ADH1B	           0
-	  4	 100239319	 T	 C	  H	  R	 ADH1B	           0.15
-	  4	 100239319	 T	 G	  H	  P	 ADH1B	           0
+	1	69134	A	C	E	A	OR4F5	0.03
+	1	69134	A	G	E	G	OR4F5	0.09
+	1	69134	A	T	E	V	OR4F5	0.03
+	4	100239319	T	A	H	L	ADH1B	0
+	4	100239319	T	C	H	R	ADH1B	0.15
+	4	100239319	T	G	H	P	ADH1B	0
 
 
-The custom galaxy datatypes for dbNSFP can automatically convert the specially formatted tabular file for use by SnpSift dbNSFP:
-  1. Upload the tabular file, set the datatype as: **"dbnsfp.tabular"**
-  2. Edit the history dataset attributes (pencil icon): Use "Convert Format" to convert the **"dbnsfp.tabular"** to the correct format for SnpSift dbnsfp: **"snpsiftdbnsfp"**.
+The uploaded tabular file should be set to datatype: "dbnsfp.tabular"
+Using "Convert Format" the "dbnsfp.tabular" can be converted to the correct format for SnpSift dbnsfp.
 
 The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp is in the SnpSift documentation.
 
diff -r 206675156f0c -r 84e33833420d tool-data/snpsift_dbnsfp.loc.sample
--- a/tool-data/snpsift_dbnsfp.loc.sample	Wed Apr 08 22:47:01 2015 -0400
+++ b/tool-data/snpsift_dbnsfp.loc.sample	Thu Apr 09 22:37:08 2015 -0400
@@ -1,3 +1,2 @@
-#id	build	description	path	annotations
-#GRCh37_dbNSFP2.4	GRCh37	GRCh37 dbNSFP2.4	/depot/snpeff/	SIFT_pred,Uniprot_acc
-#GRCh38_dbNSFP2.7	GRCh38	GRCh38 dbNSFP2.7	/depot/snpeff/	SIFT_pred,Uniprot_acc
+#id	desc	path	annotations
+#GRCh37_dbNSFP2.1	GRCh37 dbNSFP2.1	/depot/snpeff/	SIFT_pred,Uniprot_acc
diff -r 206675156f0c -r 84e33833420d tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Wed Apr 08 22:47:01 2015 -0400
+++ b/tool_data_table_conf.xml.sample	Thu Apr 09 22:37:08 2015 -0400
@@ -1,6 +1,6 @@
 <tables>
     <table name="snpsift_dbnsfp" comment_char="#">
-        <columns>dbkey, build, name, value, annotations</columns>
+        <columns>dbkey, name, value, annotations</columns>
         <file path="tool-data/snpsift_dbnsfp.loc" />
     </table>
 </tables>
diff -r 206675156f0c -r 84e33833420d tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Apr 08 22:47:01 2015 -0400
+++ b/tool_dependencies.xml	Thu Apr 09 22:37:08 2015 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="snpEff" version="4.0">
-        <repository changeset_revision="15d3951f1517" name="package_snpeff_4_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+  <package name="snpEff" version="4.0">
+      <repository changeset_revision="15d3951f1517" name="package_snpeff_4_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>