Mercurial > repos > iuc > snpsift_dbnsfp

changeset 275:6ae8f348325c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp_generic commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
author iuc
date Mon, 30 Nov 2015 21:45:25 -0500
parents 7a4ee812b877
children 417d227c5fef
files snpSift_dbnsfp.xml tool-data/snpsift_dbnsfp.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml
diffstat 4 files changed, 42 insertions(+), 25 deletions(-) [+]
line wrap: on
line diff
--- a/snpSift_dbnsfp.xml	Mon Nov 30 21:45:04 2015 -0500
+++ b/snpSift_dbnsfp.xml	Mon Nov 30 21:45:25 2015 -0500
@@ -1,5 +1,5 @@
-<tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="4.0.0">
-    <description>Add Annotations from dbNSFP</description>
+<tool id="snpSift_dbnsfp_generic" name="SnpSift dbNSFP" version="4.0.0">
+    <description>Add Annotations from dbNSFP and similar annotation DBs</description>
     <macros>
         <import>snpSift_macros.xml</import>
     </macros>
@@ -31,8 +31,8 @@
             <when value="cached">
                 <param name="dbnsfp" type="select" label="Genome">
                     <options from_data_table="snpsift_dbnsfp">
-                        <column name="name" index="1"/>
-                        <column name="value" index="2"/>
+                        <column name="name" index="2"/>
+                        <column name="value" index="3"/>
                     </options>
                 </param>
                 <param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with">
@@ -73,6 +73,7 @@
     <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
@@ -241,32 +242,47 @@
     rs numbers from UniSNP, which is a cleaned version of dbSNP build 129, in format: rs number1;rs number2;...
 
 
-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.
+
+The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp is in the SnpSift documentation:
+http://snpeff.sourceforge.net/SnpSift.html#dbNSFP
 
-However, any dbNSFP-like tabular file that be can used with SnpSift dbnsfp if it has::
+A couple dbNSFP databases are prebuilt for SnpSift at:
+http://sourceforge.net/projects/snpeff/files/databases/dbNSFP/
+
+
+
+
+**Uploading Your Own Annotations for any Genome**
 
-	- 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
+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
+
 
 For example:
 
 ::
 
 	#chr	pos(1-coor)	ref	alt	aaref	aaalt	genename	SIFT_score
-	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
+	  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 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 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 procedure for preparing the dbNSFP data for use in SnpSift dbnsfp is in the SnpSift documentation.
 
--- a/tool-data/snpsift_dbnsfp.loc.sample	Mon Nov 30 21:45:04 2015 -0500
+++ b/tool-data/snpsift_dbnsfp.loc.sample	Mon Nov 30 21:45:25 2015 -0500
@@ -1,2 +1,3 @@
-#id	desc	path	annotations
-#GRCh37_dbNSFP2.1	GRCh37 dbNSFP2.1	/depot/snpeff/	SIFT_pred,Uniprot_acc
+#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
--- a/tool_data_table_conf.xml.sample	Mon Nov 30 21:45:04 2015 -0500
+++ b/tool_data_table_conf.xml.sample	Mon Nov 30 21:45:25 2015 -0500
@@ -1,6 +1,6 @@
 <tables>
     <table name="snpsift_dbnsfp" comment_char="#">
-        <columns>dbkey, name, value, annotations</columns>
+        <columns>dbkey, build, name, value, annotations</columns>
         <file path="tool-data/snpsift_dbnsfp.loc" />
     </table>
 </tables>
--- a/tool_dependencies.xml	Mon Nov 30 21:45:04 2015 -0500
+++ b/tool_dependencies.xml	Mon Nov 30 21:45:25 2015 -0500
@@ -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>