# HG changeset patch
# User iuc
# Date 1601312456 0
# Node ID ac16d24f0d9d3db0ff909ec5130a72aca73cd1aa
# Parent  57ac42ec1be38d03c49b0461e04ad34cdf923231
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 577ea693a59004c6fa892d079cd0b2b835ee59bf"

diff -r 57ac42ec1be3 -r ac16d24f0d9d plink.xml
--- a/plink.xml	Fri Sep 25 17:48:45 2020 +0000
+++ b/plink.xml	Mon Sep 28 17:00:56 2020 +0000
@@ -51,10 +51,10 @@
         && ln -s '$inputs.inputs.bim' plink_input/plink_input.bim
         && ln -s '$inputs.inputs.fam' plink_input/plink_input.fam
     #elif $inputs.inputs.filetype == 'vcf':
-        #if $inputs.inputs.input.is_of_type('vcf'):
+        #if $inputs.inputs.input.is_of_type('bcf'):
+            && plink --bcf '$inputs.inputs.input' 
+        #else:
             && plink --vcf '$inputs.inputs.input' 
-        #else:
-            && plink --bcf '$inputs.inputs.input' 
         #end if
         --out plink_input/plink_input
     #end if
@@ -394,7 +394,7 @@
                     <param format='txt' name='fam' type='data' label='plink fam file'/>
                 </when>
                 <when value='vcf'>
-                    <param name='input' format='vcf,bcf' type='data' label='VCF/BCF Input file'/>
+                    <param name='input' format='vcf,vcf_bgzip,bcf' type='data' label='VCF/BCF Input file'/>
                 </when>
             </conditional>
             <param name='pheno' type='data' format='txt,tabular' label='Phenotype file' help='Read phenotype values from the 3rd column of the specified space- or tab-delimited file, instead of the .fam or .ped file.' optional='true'/>