# HG changeset patch
# User iuc
# Date 1642652848 0
# Node ID aa85f6cf1d16021901a6f152214443d643c2d736
# Parent  c664e42e75f82fa0d1e20a385618b7f06f3a0854
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e10d34b547557b2bd4f0be69e31204bd5703e422"

diff -r c664e42e75f8 -r aa85f6cf1d16 crossmap_bed.xml
--- a/crossmap_bed.xml	Thu Jul 15 16:14:53 2021 +0000
+++ b/crossmap_bed.xml	Thu Jan 20 04:27:28 2022 +0000
@@ -18,15 +18,15 @@
     <command><![CDATA[
 CrossMap.py bed
 '${chain_source.input_chain}'
-
 '${input}'
 
 #if $merge_unmapped_entries:
     > '${output_combined}'
 #else:
     output
+    --unmap-file output.unmap
 #end if
-
+--chromid $chromid
     ]]></command>
 
 
@@ -35,7 +35,11 @@
                help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/>
 
         <expand macro="chain" />
-
+        <param name="chromid" type="select" label="Style of chromosome IDs">
+            <option value="a" selected="true">As-is</option>
+            <option value="l">Long style, e.g. chr1, chrX</option>
+            <option value="s">Short style, e.g. 1, X</option>
+        </param>
         <param name="merge_unmapped_entries" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Merge failed and converted entries into single file"/>
     </inputs>
 
@@ -76,6 +80,7 @@
             <param name="index_source" value="history"/>
             <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
             <param name="merge_unmapped_entries" value="false" />
+            <param name="chromid" value="s" />
 
             <output name="output_valid" file="test_bed_02_output_a__only-matches.bed"/>
             <output name="output_failed" file="test_bed_02_output_a__only_fails.bed"/>
@@ -85,6 +90,7 @@
             <param name="index_source" value="history"/>
             <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
             <param name="merge_unmapped_entries" value="true" />
+            <param name="chromid" value="s" />
 
             <output name="output_combined" file="test_bed_02_output_a__all.bed"/>
         </test>
diff -r c664e42e75f8 -r aa85f6cf1d16 macros.xml
--- a/macros.xml	Thu Jul 15 16:14:53 2021 +0000
+++ b/macros.xml	Thu Jan 20 04:27:28 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 c664e42e75f8 -r aa85f6cf1d16 test-data/test_bam_01_output_a.bam
Binary file test-data/test_bam_01_output_a.bam has changed
diff -r c664e42e75f8 -r aa85f6cf1d16 test-data/test_bed_02_input_a.bed
--- a/test-data/test_bed_02_input_a.bed	Thu Jul 15 16:14:53 2021 +0000
+++ b/test-data/test_bed_02_input_a.bed	Thu Jan 20 04:27:28 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 c664e42e75f8 -r aa85f6cf1d16 test-data/test_bed_02_output_a__all.bed
--- a/test-data/test_bed_02_output_a__all.bed	Thu Jul 15 16:14:53 2021 +0000
+++ b/test-data/test_bed_02_output_a__all.bed	Thu Jan 20 04:27:28 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 c664e42e75f8 -r aa85f6cf1d16 test-data/test_bed_02_output_a__only_fails.bed
--- a/test-data/test_bed_02_output_a__only_fails.bed	Thu Jul 15 16:14:53 2021 +0000
+++ b/test-data/test_bed_02_output_a__only_fails.bed	Thu Jan 20 04:27:28 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 c664e42e75f8 -r aa85f6cf1d16 test-data/test_vcf_01_input.vcf
--- a/test-data/test_vcf_01_input.vcf	Thu Jul 15 16:14:53 2021 +0000
+++ b/test-data/test_vcf_01_input.vcf	Thu Jan 20 04:27:28 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 c664e42e75f8 -r aa85f6cf1d16 test-data/test_vcf_01_output.vcf.unmap
--- a/test-data/test_vcf_01_output.vcf.unmap	Thu Jul 15 16:14:53 2021 +0000
+++ b/test-data/test_vcf_01_output.vcf.unmap	Thu Jan 20 04:27:28 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)