diff snpSift_dbnsfp.xml @ 114:fc8a3e1e7880 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 344140b8df53b8b7024618bb04594607a045c03a

--- a/snpSift_dbnsfp.xml	Sun May 03 22:47:36 2015 -0400
+++ b/snpSift_dbnsfp.xml	Mon May 04 22:37:10 2015 -0400
@@ -1,13 +1,14 @@
 <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>
     </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
     <command>
         java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar dbnsfp -v
         #if $db.dbsrc == 'cached' :
-          -db $db.dbnsfp 
+          -db $db.dbnsfp
           #if $db.annotations and $db.annotations.__str__ != '':
             -f "$db.annotations"
           #end if
@@ -16,8 +17,8 @@
           #if $db.annotations and $db.annotations.__str__ != '':
             -f "$db.annotations"
           #end if
-        #end if          
-        $input > $output  
+        #end if
+        $input > $output
         2> tmp.err &amp;&amp; grep -v file tmp.err
     </command>
     <inputs>
@@ -53,7 +54,6 @@
             </when>
         </conditional>
     </inputs>
-    <expand macro="stdio" />
     <outputs>
         <data format="vcf" name="output" />
     </outputs>
@@ -241,13 +241,13 @@
     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 website for  dbNSFP database is https://sites.google.com/site/jpopgen/dbNSFP  and there is only annotation for human hg18 and hg19 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 line of the file must be column headers that name the annotations.
 	- The first 4 columns are required and must be::
-		1. chromosome 
+		1. chromosome
 		2. position in chromosome
 		3. reference base
 		4. alternate base