diff snpSift_dbnsfp.xml @ 76:eed6bdc8fb8c draft

Uploaded

--- a/snpSift_dbnsfp.xml	Sat Apr 18 22:37:16 2015 -0400
+++ b/snpSift_dbnsfp.xml	Sat Apr 18 22:47:27 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.