# HG changeset patch
# User iuc
# Date 1642653060 0
# Node ID eb66d7a04bf86d72095510fc946648a06f3176d8
# Parent  8635b6b8a8f27bc1b0378805aea61d0924cd6ec9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e10d34b547557b2bd4f0be69e31204bd5703e422"

diff -r 8635b6b8a8f2 -r eb66d7a04bf8 crossmap_region.xml
--- a/crossmap_region.xml	Thu Jul 15 16:19:33 2021 +0000
+++ b/crossmap_region.xml	Thu Jan 20 04:31:00 2022 +0000
@@ -10,14 +10,20 @@
 CrossMap.py region
     '${chain_source.input_chain}'
     '${input}'
+    $output
+    --chromid $chromid
     --ratio $ratio
-    '$output'
     ]]></command>
     <inputs>
         <param name="input" type="data" format="bed" label="BED file"
                help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/>
         <expand macro="chain" />
         <param argument="--ratio" type="float" min="0" max="1" value="0.85" label="Minimum ratio of bases that must remap."/>
+        <param argument="--chromid" type="select" label="Chromid" help="The style of chromosome IDs">
+            <option value="a" selected="true">Default (a)</option>
+            <option value="s">Short style (s)</option>
+            <option value="l">Long stype (l)</option>
+        </param>
     </inputs>
     <outputs>
         <data name="output" format="bed"/>
diff -r 8635b6b8a8f2 -r eb66d7a04bf8 macros.xml
--- a/macros.xml	Thu Jul 15 16:19:33 2021 +0000
+++ b/macros.xml	Thu Jan 20 04:31:00 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 8635b6b8a8f2 -r eb66d7a04bf8 test-data/test_bam_01_output_a.bam
Binary file test-data/test_bam_01_output_a.bam has changed
diff -r 8635b6b8a8f2 -r eb66d7a04bf8 test-data/test_bed_02_input_a.bed
--- a/test-data/test_bed_02_input_a.bed	Thu Jul 15 16:19:33 2021 +0000
+++ b/test-data/test_bed_02_input_a.bed	Thu Jan 20 04:31:00 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 8635b6b8a8f2 -r eb66d7a04bf8 test-data/test_bed_02_output_a__all.bed
--- a/test-data/test_bed_02_output_a__all.bed	Thu Jul 15 16:19:33 2021 +0000
+++ b/test-data/test_bed_02_output_a__all.bed	Thu Jan 20 04:31:00 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 8635b6b8a8f2 -r eb66d7a04bf8 test-data/test_bed_02_output_a__only_fails.bed
--- a/test-data/test_bed_02_output_a__only_fails.bed	Thu Jul 15 16:19:33 2021 +0000
+++ b/test-data/test_bed_02_output_a__only_fails.bed	Thu Jan 20 04:31:00 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 8635b6b8a8f2 -r eb66d7a04bf8 test-data/test_vcf_01_input.vcf
--- a/test-data/test_vcf_01_input.vcf	Thu Jul 15 16:19:33 2021 +0000
+++ b/test-data/test_vcf_01_input.vcf	Thu Jan 20 04:31:00 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 8635b6b8a8f2 -r eb66d7a04bf8 test-data/test_vcf_01_output.vcf.unmap
--- a/test-data/test_vcf_01_output.vcf.unmap	Thu Jul 15 16:19:33 2021 +0000
+++ b/test-data/test_vcf_01_output.vcf.unmap	Thu Jan 20 04:31:00 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)