# HG changeset patch
# User iuc
# Date 1601397800 0
# Node ID 18be55ee8e08fe7d08b7f0732c4639614ccc860a
# Parent  ac16d24f0d9d3db0ff909ec5130a72aca73cd1aa
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"

diff -r ac16d24f0d9d -r 18be55ee8e08 plink.xml
--- a/plink.xml	Mon Sep 28 17:00:56 2020 +0000
+++ b/plink.xml	Tue Sep 29 16:43:20 2020 +0000
@@ -46,18 +46,7 @@
     ## Create Plink folder for any inputs
     mkdir ./plink_output
     && mkdir ./plink_input
-    #if $inputs.inputs.filetype == 'bfile':
-        && ln -s '$inputs.inputs.bed' plink_input/plink_input.bed
-        && 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 $inputs.inputs.input.is_of_type('bcf'):
-            && plink --bcf '$inputs.inputs.input' 
-        #else:
-            && plink --vcf '$inputs.inputs.input' 
-        #end if
-        --out plink_input/plink_input
-    #end if
+
 
     ## If bmerge is set, create folder for merged files
     #if $functions.func == 'data_manage':
@@ -69,9 +58,21 @@
         #end if
     #end if
 
-    ## Plink commands by section
 
-    && plink --bfile plink_input/plink_input
+    #if $inputs.inputs.filetype == 'bfile':
+        && ln -s '$inputs.inputs.bed' plink_input/plink_input.bed
+        && ln -s '$inputs.inputs.bim' plink_input/plink_input.bim
+        && ln -s '$inputs.inputs.fam' plink_input/plink_input.fam
+        && plink --bfile plink_input/plink_input
+    #elif $inputs.inputs.filetype == 'vcf':
+        #if $inputs.inputs.input.is_of_type('bcf'):
+            && plink --bcf '$inputs.inputs.input' 
+        #else:
+            && plink --vcf '$inputs.inputs.input' 
+        #end if
+    #end if
+
+    ## Plink commands by section
     #if $inputs.covar_input:
             --covar '$inputs.covar_input'
     #end if