# HG changeset patch
# User iuc
# Date 1579784668 18000
# Node ID 84959112d9a6b39934770f371c9f005e4c50d269
# Parent  70bc6ced57f7064fb36d0ad5ada6d21b92e3702f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 36e9065027cc7bf721e9d203208477ee88906c57"

diff -r 70bc6ced57f7 -r 84959112d9a6 macros.xml
--- a/macros.xml	Mon Mar 26 12:20:23 2018 -0400
+++ b/macros.xml	Thu Jan 23 08:04:28 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 70bc6ced57f7 -r 84959112d9a6 test-data/vcfannotategenotypes-test1.vcf
--- a/test-data/vcfannotategenotypes-test1.vcf	Mon Mar 26 12:20:23 2018 -0400
+++ b/test-data/vcfannotategenotypes-test1.vcf	Thu Jan 23 08:04:28 2020 -0500
@@ -22,12 +22,12 @@
 ##INFO=<ID=added-genotypes.has_variant,Number=0,Type=Flag,Description="True if added-genotypes has a called alternate among samples under comparison.">
 ##FORMAT=<ID=added-genotypes,Number=1,Type=String,Description="Genotype from added-genotypes.">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
-19	111	.	A	C	9.6	.	added-genotypes.has_variant	GT:HQ:added-genotypes	0|0:10,10:0/0	0|0:10,10:./.	0/1:3,3:0/1
-19	112	.	A	G	10	.	added-genotypes.has_variant	GT:HQ:added-genotypes	0|0:10,10:0/0	0|0:10,10:./.	0/1:3,3:0/1
-20	14370	rs6054257	G	A	29	PASS	AF=0.5;DP=14;NS=3;DB;H2;added-genotypes.has_variant	GT:GQ:DP:HQ:added-genotypes	0|0:48:1:51,51:0/0	1|0:48:8:51,51:./.	1/1:43:5:.,.:1/1
-20	17330	.	T	A	3	q10	AF=0.017;DP=11;NS=3;added-genotypes.has_variant	GT:GQ:DP:HQ:added-genotypes	0|0:49:3:58,50:0/0	0|1:3:5:65,3:./.	0/0:41:3:.,.:0/0
-20	1110696	rs6040355	A	G,T	67	PASS	AA=T;AF=0.333,0.667;DP=10;NS=2;DB;added-genotypes.has_variant	GT:GQ:DP:HQ:added-genotypes	1|2:21:6:23,27:1/2	2|1:2:0:18,2:./.	2/2:35:4:.,.:2/2
-20	1230237	.	T	.	47	PASS	AA=T;DP=13;NS=3;added-genotypes.has_variant	GT:GQ:DP:HQ:added-genotypes	0|0:54:.:56,60:0/0	0|0:48:4:51,51:./.	0/0:61:2:.,.:0/0
+19	111	.	A	C	9.6	.	added-genotypes.has_variant	GT:HQ:added-genotypes	0|0:10,10:0|0	0|0:10,10:./.	0/1:3,3:0/1
+19	112	.	A	G	10	.	added-genotypes.has_variant	GT:HQ:added-genotypes	0|0:10,10:0|0	0|0:10,10:./.	0/1:3,3:0/1
+20	14370	rs6054257	G	A	29	PASS	AF=0.5;DP=14;NS=3;DB;H2;added-genotypes.has_variant	GT:GQ:DP:HQ:added-genotypes	0|0:48:1:51,51:0|0	1|0:48:8:51,51:./.	1/1:43:5:.,.:1/1
+20	17330	.	T	A	3	q10	AF=0.017;DP=11;NS=3;added-genotypes.has_variant	GT:GQ:DP:HQ:added-genotypes	0|0:49:3:58,50:0|0	0|1:3:5:65,3:./.	0/0:41:3:.,.:0/0
+20	1110696	rs6040355	A	G,T	67	PASS	AA=T;AF=0.333,0.667;DP=10;NS=2;DB;added-genotypes.has_variant	GT:GQ:DP:HQ:added-genotypes	1|2:21:6:23,27:1|2	2|1:2:0:18,2:./.	2/2:35:4:.,.:2/2
+20	1230237	.	T	.	47	PASS	AA=T;DP=13;NS=3;added-genotypes.has_variant	GT:GQ:DP:HQ:added-genotypes	0|0:54:.:56,60:0|0	0|0:48:4:51,51:./.	0/0:61:2:.,.:0/0
 20	1234567	microsat1	G	GA,GAC	50	PASS	AA=G;AC=3,1;AN=6;DP=9;NS=3;added-genotypes.has_variant	GT:GQ:DP:added-genotypes	0/1:.:4:0/1	0/2:17:2:./.	1/1:40:3:1/1
 20	1235237	.	T	.	0	.	added-genotypes.has_variant	GT:added-genotypes	0/0:0/0	0|0:./.	./.:.
-X	10	rsTest	AC	A,ATG	10	PASS	added-genotypes.has_variant	GT:added-genotypes	0:0	0/1:./.	0|2:0/2
+X	10	rsTest	AC	A,ATG	10	PASS	added-genotypes.has_variant	GT:added-genotypes	0:0	0/1:./.	0|2:0|2
diff -r 70bc6ced57f7 -r 84959112d9a6 vcfannotategenotypes.xml
--- a/vcfannotategenotypes.xml	Mon Mar 26 12:20:23 2018 -0400
+++ b/vcfannotategenotypes.xml	Thu Jan 23 08:04:28 2020 -0500
@@ -5,7 +5,7 @@
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio" />
-  <command>vcfannotategenotypes "${tag_option}" "${input1}" "${input2}" > "${out_file1}"</command>
+  <command>vcfannotategenotypes '${tag_option}' '${input1}' '${input2}' > '${out_file1}'</command>
   <inputs>
     <param format="vcf" name="input1" type="data" label="Annotate genotypes in" help="First VCF dataset"/>
     <param format="vcf" name="input2" type="data" label="using genotypes from" help="Second VCF dataset"/>