# HG changeset patch
# User jjohnson
# Date 1531844496 14400
# Node ID fd612f8119a2506c4991816ea63a0c59a4c44b6b
# Parent  d5cb252c68dad4fd8c91fb90a9004c0d2e6336c4
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit f003aece24587f68b883449f278f1e601110e2ec-dirty

diff -r d5cb252c68da -r fd612f8119a2 ensembl_variant_report.py
--- a/ensembl_variant_report.py	Thu Jun 14 18:07:10 2018 -0400
+++ b/ensembl_variant_report.py	Tue Jul 17 12:21:36 2018 -0400
@@ -96,7 +96,8 @@
             dp = int(fields[di])
             dpr = [int(x) for x in fields[fi].split(',')]
             for i,alt in enumerate(alts.split(',')):
-                freq = float(dpr[i+1])/float(sum(dpr)) if dpr else None
+                freq = float(dpr[i+1])/float(dp) if dp and dpr else \
+                    float(dpr[i+1])/float(sum(dpr)) if dpr else None
                 yield (transcript,pos,ref,alt,dp,freq)
 
     def parse_snpeff_vcf():
@@ -131,7 +132,8 @@
                                 (eff, effs) = effect.rstrip(')').split('(')
                                 (impact, functional_class, codon_change, aa_change, aa_len, gene_name, biotype, coding, transcript, exon, alt) = effs.split('|')[0:11]
                             i = alt_list.index(alt) if alt in alt_list else 0
-                            freq = float(dpr[i+1])/float(sum(dpr)) if dpr else None
+                            freq = float(dpr[i+1])/float(dp) if dp and dpr else \
+                                float(dpr[i+1])/float(sum(dpr)) if dpr else None
                             yield (transcript,pos,ref,alt,dp,freq)
 
 
diff -r d5cb252c68da -r fd612f8119a2 ensembl_variant_report.xml
--- a/ensembl_variant_report.xml	Thu Jun 14 18:07:10 2018 -0400
+++ b/ensembl_variant_report.xml	Tue Jul 17 12:21:36 2018 -0400
@@ -94,7 +94,12 @@
         
     </inputs>
     <outputs>
-        <data name="output" format="tabular" />
+        <data name="output" format="tabular" >
+            <actions>
+                <action name="column_names" type="metadata" 
+                 default="Gene,Ref_location,Ref_seq,Var_seq,Frequency,DP,Ensemble_Gene_transcript,AA_pos,AA_var,Protein_len,Stop_Codon,Variant_Peptide,Transcipt_type"/>
+            </actions>
+        </data>
     </outputs>
     <tests>
         <test>