diff pileup_to_vcf.xml @ 9:c0a6e8f595ec default tip

Add option to set VCF ID field value, this can be used to ID germline variants for SnpSift

--- a/pileup_to_vcf.xml	Thu Mar 28 14:55:50 2013 -0500
+++ b/pileup_to_vcf.xml	Thu Apr 11 10:28:10 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="pileup_to_vcf" name="Pileup to VCF" version="2.1">
+<tool id="pileup_to_vcf" name="Pileup to VCF" version="2.2">
   <description>Converts a pileup to VCF with filtering</description>
   <command interpreter="python">pileup_to_vcf.py -i $input_file -o $output_file 
     #if $min_cvrg.__str__  != '':
@@ -15,6 +15,9 @@
     #end if
     $allow_multiples
     $snps_only
+    #if $vcf_id.__str__ != '':
+      --id $vcf_id
+    #end if
     #if $cols.select_order == 'yes' :
       #if $chrom_col.__str__  != '':
         --chrom_col $chrom_col 
@@ -65,6 +68,9 @@
       <option value="qual">Reads at this position taht pass the base call quality threshold</option>
       <option value="all">All reads and indels</option>
     </param>
+    <param name="vcf_id" type="text" optional="true" value="" label="The VCF ID" help="The VCF output will use this as the ID field value">
+      <validator type="regex" message="whitespace characters not allowed">^\S*$</validator>
+    </param>
   </inputs>
   <outputs>
     <data format="vcf" metadata_source="input_file" name="output_file" />