# HG changeset patch
# User iuc
# Date 1579784449 18000
# Node ID 285060661b452f0436032dab95fc5d66dcf55e96
# Parent  e92b3c0f92241a070ef3ebdfbc267ea5e65c6139
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv commit 36e9065027cc7bf721e9d203208477ee88906c57"

diff -r e92b3c0f9224 -r 285060661b45 macros.xml
--- a/macros.xml	Mon Mar 26 12:17:07 2018 -0400
+++ b/macros.xml	Thu Jan 23 08:00:49 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 e92b3c0f9224 -r 285060661b45 test-data/vcf2tsv-test1.tab
--- a/test-data/vcf2tsv-test1.tab	Mon Mar 26 12:17:07 2018 -0400
+++ b/test-data/vcf2tsv-test1.tab	Thu Jan 23 08:00:49 2020 -0500
@@ -1,28 +1,37 @@
-CHROM	POS	ID	REF	ALT	QUAL	FILTER	AA	AC	AF	AN	DP	NS	DB	H2	SAMPLE	DP	GQ	GT	HQ
-19	111	.	A	C	9.6	.	.	.	.	.	.	.	0	0	NA00001	.	.	0|0	10,10
-19	111	.	A	C	9.6	.	.	.	.	.	.	.	0	0	NA00002	.	.	0|0	10,10
-19	111	.	A	C	9.6	.	.	.	.	.	.	.	0	0	NA00003	.	.	0/1	3,3
-19	112	.	A	G	10	.	.	.	.	.	.	.	0	0	NA00001	.	.	0|0	10,10
-19	112	.	A	G	10	.	.	.	.	.	.	.	0	0	NA00002	.	.	0|0	10,10
-19	112	.	A	G	10	.	.	.	.	.	.	.	0	0	NA00003	.	.	0/1	3,3
-20	14370	rs6054257	G	A	29	PASS	.	.	0.5	.	14	3	1	1	NA00001	1	48	0|0	51,51
-20	14370	rs6054257	G	A	29	PASS	.	.	0.5	.	14	3	1	1	NA00002	8	48	1|0	51,51
-20	14370	rs6054257	G	A	29	PASS	.	.	0.5	.	14	3	1	1	NA00003	5	43	1/1	.,.
-20	17330	.	T	A	3	q10	.	.	0.017	.	11	3	0	0	NA00001	3	49	0|0	58,50
-20	17330	.	T	A	3	q10	.	.	0.017	.	11	3	0	0	NA00002	5	3	0|1	65,3
-20	17330	.	T	A	3	q10	.	.	0.017	.	11	3	0	0	NA00003	3	41	0/0	.,.
-20	1110696	rs6040355	A	G,T	67	PASS	T	.	0.333,0.667	.	10	2	1	0	NA00001	6	21	1|2	23,27
-20	1110696	rs6040355	A	G,T	67	PASS	T	.	0.333,0.667	.	10	2	1	0	NA00002	0	2	2|1	18,2
-20	1110696	rs6040355	A	G,T	67	PASS	T	.	0.333,0.667	.	10	2	1	0	NA00003	4	35	2/2	.,.
-20	1230237	.	T	.	47	PASS	T	.	.	.	13	3	0	0	NA00001	.	54	0|0	56,60
-20	1230237	.	T	.	47	PASS	T	.	.	.	13	3	0	0	NA00002	4	48	0|0	51,51
-20	1230237	.	T	.	47	PASS	T	.	.	.	13	3	0	0	NA00003	2	61	0/0	.,.
-20	1234567	microsat1	G	GA,GAC	50	PASS	G	3,1	.	6	9	3	0	0	NA00001	4	.	0/1	.
-20	1234567	microsat1	G	GA,GAC	50	PASS	G	3,1	.	6	9	3	0	0	NA00002	2	17	0/2	.
-20	1234567	microsat1	G	GA,GAC	50	PASS	G	3,1	.	6	9	3	0	0	NA00003	3	40	1/1	.
-20	1235237	.	T	.	0	.	.	.	.	.	.	.	0	0	NA00001	.	.	0/0	.
-20	1235237	.	T	.	0	.	.	.	.	.	.	.	0	0	NA00002	.	.	0|0	.
-20	1235237	.	T	.	0	.	.	.	.	.	.	.	0	0	NA00003	.	.	./.	.
-X	10	rsTest	AC	A,ATG	10	PASS	.	.	.	.	.	.	0	0	NA00001	.	.	0	.
-X	10	rsTest	AC	A,ATG	10	PASS	.	.	.	.	.	.	0	0	NA00002	.	.	0/1	.
-X	10	rsTest	AC	A,ATG	10	PASS	.	.	.	.	.	.	0	0	NA00003	.	.	0|2	.
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	AA	AC	AF	AN	DB	DP	H2	NS	SAMPLE	DP	GQ	GT	HQ
+19	111	.	A	C	9.6	.	.	.	.	.	.	.	.	.	NA00001	.	.	0|0	10,10
+19	111	.	A	C	9.6	.	.	.	.	.	.	.	.	.	NA00002	.	.	0|0	10,10
+19	111	.	A	C	9.6	.	.	.	.	.	.	.	.	.	NA00003	.	.	0/1	3,3
+19	112	.	A	G	10	.	.	.	.	.	.	.	.	.	NA00001	.	.	0|0	10,10
+19	112	.	A	G	10	.	.	.	.	.	.	.	.	.	NA00002	.	.	0|0	10,10
+19	112	.	A	G	10	.	.	.	.	.	.	.	.	.	NA00003	.	.	0/1	3,3
+20	14370	rs6054257	G	A	29	PASS	.	.	0.5	.	.	14	.	3	NA00001	1	48	0|0	51,51
+20	14370	rs6054257	G	A	29	PASS	.	.	0.5	.	.	14	.	3	NA00002	8	48	1|0	51,51
+20	14370	rs6054257	G	A	29	PASS	.	.	0.5	.	.	14	.	3	NA00003	5	43	1/1	.,.
+20	17330	.	T	A	3	q10	.	.	0.017	.	.	11	.	3	NA00001	3	49	0|0	58,50
+20	17330	.	T	A	3	q10	.	.	0.017	.	.	11	.	3	NA00002	5	3	0|1	65,3
+20	17330	.	T	A	3	q10	.	.	0.017	.	.	11	.	3	NA00003	3	41	0/0	.,.
+20	1110696	rs6040355	A	G	67	PASS	T	.	0.333,0.667	.	.	10	.	2	NA00001	6	21	1|2	23,27
+20	1110696	rs6040355	A	G	67	PASS	T	.	0.333,0.667	.	.	10	.	2	NA00002	0	2	2|1	18,2
+20	1110696	rs6040355	A	G	67	PASS	T	.	0.333,0.667	.	.	10	.	2	NA00003	4	35	2/2	.,.
+20	1110696	rs6040355	A	T	67	PASS	T	.	0.333,0.667	.	.	10	.	2	NA00001	6	21	1|2	23,27
+20	1110696	rs6040355	A	T	67	PASS	T	.	0.333,0.667	.	.	10	.	2	NA00002	0	2	2|1	18,2
+20	1110696	rs6040355	A	T	67	PASS	T	.	0.333,0.667	.	.	10	.	2	NA00003	4	35	2/2	.,.
+20	1230237	.	T	.	47	PASS	T	.	.	.	.	13	.	3	NA00001	.	54	0|0	56,60
+20	1230237	.	T	.	47	PASS	T	.	.	.	.	13	.	3	NA00002	4	48	0|0	51,51
+20	1230237	.	T	.	47	PASS	T	.	.	.	.	13	.	3	NA00003	2	61	0/0	.,.
+20	1234567	microsat1	G	GA	50	PASS	G	3,1	.	6	.	9	.	3	NA00001	4	.	0/1	.
+20	1234567	microsat1	G	GA	50	PASS	G	3,1	.	6	.	9	.	3	NA00002	2	17	0/2	.
+20	1234567	microsat1	G	GA	50	PASS	G	3,1	.	6	.	9	.	3	NA00003	3	40	1/1	.
+20	1234567	microsat1	G	GAC	50	PASS	G	3,1	.	6	.	9	.	3	NA00001	4	.	0/1	.
+20	1234567	microsat1	G	GAC	50	PASS	G	3,1	.	6	.	9	.	3	NA00002	2	17	0/2	.
+20	1234567	microsat1	G	GAC	50	PASS	G	3,1	.	6	.	9	.	3	NA00003	3	40	1/1	.
+20	1235237	.	T	.	0	.	.	.	.	.	.	.	.	.	NA00001	.	.	0/0	.
+20	1235237	.	T	.	0	.	.	.	.	.	.	.	.	.	NA00002	.	.	0|0	.
+20	1235237	.	T	.	0	.	.	.	.	.	.	.	.	.	NA00003	.	.	./.	.
+X	10	rsTest	AC	A	10	PASS	.	.	.	.	.	.	.	.	NA00001	.	.	0	.
+X	10	rsTest	AC	A	10	PASS	.	.	.	.	.	.	.	.	NA00002	.	.	0/1	.
+X	10	rsTest	AC	A	10	PASS	.	.	.	.	.	.	.	.	NA00003	.	.	0|2	.
+X	10	rsTest	AC	ATG	10	PASS	.	.	.	.	.	.	.	.	NA00001	.	.	0	.
+X	10	rsTest	AC	ATG	10	PASS	.	.	.	.	.	.	.	.	NA00002	.	.	0/1	.
+X	10	rsTest	AC	ATG	10	PASS	.	.	.	.	.	.	.	.	NA00003	.	.	0|2	.
diff -r e92b3c0f9224 -r 285060661b45 test-data/vcf2tsv-test2.tab
--- a/test-data/vcf2tsv-test2.tab	Mon Mar 26 12:17:07 2018 -0400
+++ b/test-data/vcf2tsv-test2.tab	Thu Jan 23 08:00:49 2020 -0500
@@ -1,13 +1,13 @@
-CHROM	POS	ID	REF	ALT	QUAL	FILTER	AA	AC	AF	AN	DP	NS	DB	H2
-19	111	.	A	C	9.6	.	.	.	.	.	.	.	0	0
-19	112	.	A	G	10	.	.	.	.	.	.	.	0	0
-20	14370	rs6054257	G	A	29	PASS	.	.	0.5	.	14	3	1	1
-20	17330	.	T	A	3	q10	.	.	0.017	.	11	3	0	0
-20	1110696	rs6040355	A	G	67	PASS	T	.	0.333	.	10	2	1	0
-20	1110696	rs6040355	A	T	67	PASS	T	.	0.667	.	10	2	1	0
-20	1230237	.	T	.	47	PASS	T	.	.	.	13	3	0	0
-20	1234567	microsat1	G	GA	50	PASS	G	3	.	6	9	3	0	0
-20	1234567	microsat1	G	GAC	50	PASS	G	1	.	6	9	3	0	0
-20	1235237	.	T	.	0	.	.	.	.	.	.	.	0	0
-X	10	rsTest	AC	A	10	PASS	.	.	.	.	.	.	0	0
-X	10	rsTest	AC	ATG	10	PASS	.	.	.	.	.	.	0	0
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	AA	AC	AF	AN	DB	DP	H2	NS
+19	111	.	A	C	9.6	.	.	.	.	.	.	.	.	.
+19	112	.	A	G	10	.	.	.	.	.	.	.	.	.
+20	14370	rs6054257	G	A	29	PASS	.	.	0.5	.	.	14	.	3
+20	17330	.	T	A	3	q10	.	.	0.017	.	.	11	.	3
+20	1110696	rs6040355	A	G	67	PASS	T	.	0.333,0.667	.	.	10	.	2
+20	1110696	rs6040355	A	T	67	PASS	T	.	0.333,0.667	.	.	10	.	2
+20	1230237	.	T	.	47	PASS	T	.	.	.	.	13	.	3
+20	1234567	microsat1	G	GA	50	PASS	G	3,1	.	6	.	9	.	3
+20	1234567	microsat1	G	GAC	50	PASS	G	3,1	.	6	.	9	.	3
+20	1235237	.	T	.	0	.	.	.	.	.	.	.	.	.
+X	10	rsTest	AC	A	10	PASS	.	.	.	.	.	.	.	.
+X	10	rsTest	AC	ATG	10	PASS	.	.	.	.	.	.	.	.