# HG changeset patch
# User iuc
# Date 1579784954 18000
# Node ID a60ae8af21a14e363ff5bd89204c7a7c48805655
# Parent  f5653ed90dfdbecf1f799e66727306e49d22d505
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes commit 36e9065027cc7bf721e9d203208477ee88906c57"

diff -r f5653ed90dfd -r a60ae8af21a1 macros.xml
--- a/macros.xml	Mon Mar 26 12:26:49 2018 -0400
+++ b/macros.xml	Thu Jan 23 08:09:14 2020 -0500
@@ -1,7 +1,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.0.0_rc1">vcflib</requirement>
+            <requirement type="package" version="1.0.0_rc3">vcflib</requirement>
             <yield/>
         </requirements>
     </xml>
@@ -10,10 +10,10 @@
             <exit_code range="1:" level="fatal" />
         </stdio>
     </xml>
-   <token name="@WRAPPER_VERSION@">1.0.0_rc1</token>
-   	<xml name="citations">
-   	     <citations>
-             <citation type="bibtex">
+   <token name="@WRAPPER_VERSION@">1.0.0_rc3</token>
+       <xml name="citations">
+           <citations>
+               <citation type="bibtex">
 @misc{Garrison2015,
   author = {Garrison, Erik},
   year = {2015},
@@ -22,8 +22,8 @@
   journal = {GitHub repository},
   url = {https://github.com/ekg/vcflib},
 }
-             </citation>
-   	     </citations>
-   	</xml>
+            </citation>
+        </citations>
+        </xml>
     <token name="@IS_PART_OF_VCFLIB@">is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).</token>
 </macros>
diff -r f5653ed90dfd -r a60ae8af21a1 test-data/vcfgenotypes-test1.tab
--- a/test-data/vcfgenotypes-test1.tab	Mon Mar 26 12:26:49 2018 -0400
+++ b/test-data/vcfgenotypes-test1.tab	Thu Jan 23 08:09:14 2020 -0500
@@ -1,9 +1,9 @@
 19	111	A	C	A,C	NA00001:A/A	NA00002:A/A	NA00003:A/C	
 19	112	A	G	A,G	NA00001:A/A	NA00002:A/A	NA00003:A/G	
-20	14370	G	A	G,A	NA00001:G/G	NA00002:A/G	NA00003:A/A	
+20	14370	G	A	G,A	NA00001:G/G	NA00002:G/A	NA00003:A/A	
 20	17330	T	A	T,A	NA00001:T/T	NA00002:T/A	NA00003:T/T	
-20	1110696	A	G,T	A,G,T	NA00001:G/T	NA00002:T/G	NA00003:T/T	
+20	1110696	A	G,T	A,G,T	NA00001:G/T	NA00002:G/T	NA00003:T/T	
 20	1230237	T	.	T,.	NA00001:T/T	NA00002:T/T	NA00003:T/T	
 20	1234567	G	GA,GAC	G,GA,GAC	NA00001:G/GA	NA00002:G/GAC	NA00003:GA/GA	
-20	1235237	T	.	T,.	NA00001:T/T	NA00002:T/T	NA00003:T/T	
+20	1235237	T	.	T,.	NA00001:T/T	NA00002:T/T	NA00003:./.	
 X	10	AC	A,ATG	AC,A,ATG	NA00001:AC	NA00002:AC/A	NA00003:AC/ATG	
diff -r f5653ed90dfd -r a60ae8af21a1 vcfgenotypes.xml
--- a/vcfgenotypes.xml	Mon Mar 26 12:26:49 2018 -0400
+++ b/vcfgenotypes.xml	Thu Jan 23 08:09:14 2020 -0500
@@ -5,7 +5,7 @@
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio" />
-  <command>vcfgenotypes "${vcf_input}" > "${out_file1}"</command>
+  <command>vcfgenotypes '${vcf_input}' > '${out_file1}'</command>
   <inputs>
     <param format="vcf" name="vcf_input" type="data" label="Select VCF dataset"/>
   </inputs>