diff VCF_to_VariantDB.xml @ 7:04e3bba317f4 draft

Added selection to differentiate in VCF format

--- a/VCF_to_VariantDB.xml	Fri Feb 21 07:17:28 2014 -0500
+++ b/VCF_to_VariantDB.xml	Thu Jun 05 04:02:28 2014 -0400
@@ -42,14 +42,21 @@
 
       ## The server to send results to
 	-S $server
-  
+      ## The input file format
+	-F $format 
       
   </command>
   <requirements>
 	<requirement type="package">tabix</requirement>
   </requirements>
   <inputs>
-        <param name="input1" type="data" format="vcf" label="VCF file" help="Unified Genotyper VCF File" />
+        <param name="input1" type="data" format="vcf" label="VCF file" help="Select variant file to import" />
+	<param name="format" type="select" label="VCF Source Application" help="Supported formats are VCF from UnifiedGenotyper, HaplotypeCaller, Mutect and VarScan">
+		<option value="UG">GATK Unified Genotyper</option>
+		<option value="HC">GATK Haplotype Caller</option>
+		<option value="MT">GATK MuTect</option>
+		<option value="VS">Samtools VarScan</option>
+	</param>
 	<conditional name="sendData">
 	  <param name="store" type="select" label="Store VCF and BAM Files:" help="This option allows you to send the BAM and VCF files to our storage server for dynamic loading into IGV. If you store them there, please delete them here." >
 		<option value="false">No</option>
@@ -58,6 +65,7 @@
  	  <when value="true">
 		<param name="bamfile" type="data" format="bam" label="BAM File." />
 	  </when>
+	  <when value="false" />
         </conditional>
 
 	<conditional name="namefromselect">
@@ -72,6 +80,7 @@
 	  <when value="other">
 		<param name="namefile" type="data" format="sam,bam,fastq,fasta,bed,fastqsanger,fastqillumina,txt,vcf" label="Select a file from the history to base the sample name upon" />
 	  </when>
+	  <when value="vcf"/>
         </conditional>
 	<param name="samplegender" type="select" label="Sample Gender: " help="This can be set from the database frontend as well.">
 		<option value="undef">Unspecified</option>
@@ -89,7 +98,7 @@
 
 **What it does**
 
-This tools sends the results from the GATK unified genotyper to a VariantDB server. From there, variants can be compared between samples, filtered on various annotations etc.  To add servers, specify them in the tool configuration XML file. 
+This tools sends VCF files with results from the GATK unified genotyper, HaploType Caller, Mutect or samtools VarScan to a VariantDB server. From there, variants can be compared between samples, filtered on various annotations etc.  To add servers, specify them in the tool configuration XML file. 
 
 ------