# HG changeset patch
# User iuc
# Date 1642652968 0
# Node ID 5e3b182af35c55b96a33f3bdc71c806fac263200
# Parent  c413cbb69f3c95754c403194ea40f2c430b38a95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e10d34b547557b2bd4f0be69e31204bd5703e422"

diff -r c413cbb69f3c -r 5e3b182af35c macros.xml
--- a/macros.xml	Wed Nov 24 21:56:43 2021 +0000
+++ b/macros.xml	Thu Jan 20 04:29:28 2022 +0000
@@ -6,7 +6,7 @@
             <yield/>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">0.5.2</token>
+    <token name="@TOOL_VERSION@">0.6.1</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="stdio">
         <stdio>
diff -r c413cbb69f3c -r 5e3b182af35c test-data/test_bam_01_output_a.bam
Binary file test-data/test_bam_01_output_a.bam has changed
diff -r c413cbb69f3c -r 5e3b182af35c test-data/test_bed_02_input_a.bed
--- a/test-data/test_bed_02_input_a.bed	Wed Nov 24 21:56:43 2021 +0000
+++ b/test-data/test_bed_02_input_a.bed	Thu Jan 20 04:29:28 2022 +0000
@@ -1,5 +1,5 @@
-chr1	100	10000
-chr2	100	10000
-chr3	100	10000
-chr4	8941700 8947200 
-chr5	1	100000000
\ No newline at end of file
+1	100	10000
+2	100	10000
+3	100	10000
+4	8941700 8947200
+5	1	100000000
diff -r c413cbb69f3c -r 5e3b182af35c test-data/test_bed_02_output_a__all.bed
--- a/test-data/test_bed_02_output_a__all.bed	Wed Nov 24 21:56:43 2021 +0000
+++ b/test-data/test_bed_02_output_a__all.bed	Thu Jan 20 04:29:28 2022 +0000
@@ -1,5 +1,5 @@
-chr1	100	10000	Unmap
-chr2	100	10000	Unmap
-chr3	100	10000	Unmap
-chr4	8941700 8947200	Unmap
-chr5	1	100000000	Unmap
+1	100	10000	Unmap
+2	100	10000	Unmap
+3	100	10000	Unmap
+4	8941700 8947200	Unmap
+5	1	100000000	Unmap
diff -r c413cbb69f3c -r 5e3b182af35c test-data/test_bed_02_output_a__only_fails.bed
--- a/test-data/test_bed_02_output_a__only_fails.bed	Wed Nov 24 21:56:43 2021 +0000
+++ b/test-data/test_bed_02_output_a__only_fails.bed	Thu Jan 20 04:29:28 2022 +0000
@@ -1,5 +1,5 @@
-chr1	100	10000	Unmap
-chr2	100	10000	Unmap
-chr3	100	10000	Unmap
-chr4	8941700 8947200	Unmap
-chr5	1	100000000	Unmap
+1	100	10000	Unmap
+2	100	10000	Unmap
+3	100	10000	Unmap
+4	8941700 8947200	Unmap
+5	1	100000000	Unmap
diff -r c413cbb69f3c -r 5e3b182af35c test-data/test_vcf_01_input.vcf
--- a/test-data/test_vcf_01_input.vcf	Wed Nov 24 21:56:43 2021 +0000
+++ b/test-data/test_vcf_01_input.vcf	Thu Jan 20 04:29:28 2022 +0000
@@ -2,6 +2,7 @@
 ##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype">
 ##FORMAT=<ID=GP,Number=G,Type=Float,Description="Genotype Probabilities">
 ##FORMAT=<ID=PL,Number=G,Type=Float,Description="Phred-scaled Genotype Likelihoods">
+##contig=<ID=1,length=195471971>
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMP001	SAMP002
 1	10	rs11449	G	A	.	PASS	.	GT	0/0	0/1
 1	100 rs84825 C	C	.	PASS	.	GT:GP	0/1:.	0/1:0.03,0.97,0
diff -r c413cbb69f3c -r 5e3b182af35c test-data/test_vcf_01_output.vcf.unmap
--- a/test-data/test_vcf_01_output.vcf.unmap	Wed Nov 24 21:56:43 2021 +0000
+++ b/test-data/test_vcf_01_output.vcf.unmap	Thu Jan 20 04:29:28 2022 +0000
@@ -2,5 +2,6 @@
 ##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype">
 ##FORMAT=<ID=GP,Number=G,Type=Float,Description="Genotype Probabilities">
 ##FORMAT=<ID=PL,Number=G,Type=Float,Description="Phred-scaled Genotype Likelihoods">
+##contig=<ID=1,length=195471971>
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMP001	SAMP002
 1	200 rs84823 T	G	.	PASS	.	GT:PL	./.:.	1/1:10,5,0	Fail(REF==ALT)