# HG changeset patch
# User iuc
# Date 1626366006 0
# Node ID 71730c177cdf866ceb6255dcbfcd1ce712bb59f3
# Parent  b21851ddcc794527ae0efd98ba7828ae2ea66453
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"

diff -r b21851ddcc79 -r 71730c177cdf crossmap_vcf.xml
--- a/crossmap_vcf.xml	Wed Sep 30 13:59:28 2020 +0000
+++ b/crossmap_vcf.xml	Thu Jul 15 16:20:06 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="crossmap_vcf" name="CrossMap VCF" version="@WRAPPER_VERSION@">
+<tool id="crossmap_vcf" name="CrossMap VCF" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
     <description>Convert genome coordinates or annotation files between genome assemblies</description>
     <macros>
         <import>macros.xml</import>
@@ -21,7 +21,7 @@
 
 '${input_file}'
 '${seq_source.input_fasta}'
-
+$no_comp_alleles
 output
     ]]></command>
 
@@ -54,6 +54,7 @@
                 <expand macro="chain" />
             </when>
         </conditional>
+        <param argument="--no-comp-alleles" type="boolean" truevalue="" falsevalue="--no-comp-alleles" checked="true" label="Check if the reference allele is different from the alternate allele"/>
     </inputs>
 
     <outputs>
@@ -72,8 +73,8 @@
             <output name="output">
                 <assert_contents>
                     <has_text text="##fileformat=VCFv4.2"/>
-                    <has_text text="##liftOverProgram=CrossMap(https://sourceforge.net/projects/crossmap/)"/>
-                    <has_text text="##new_reference_genome="/>
+                    <has_text_matching expression="##liftOverProgram=&lt;CrossMap,version=[0-9.]+,website=https://sourceforge.net/projects/crossmap&gt;"/>
+                    <has_text text="##targetRefGenome="/>
                     <has_text text="#CHROM"/>
                     <has_text_matching expression="2.*?rs11449.*?PASS"/>
                     <has_text_matching expression="2.*?rs84825.*?PASS"/>
diff -r b21851ddcc79 -r 71730c177cdf macros.xml
--- a/macros.xml	Wed Sep 30 13:59:28 2020 +0000
+++ b/macros.xml	Thu Jul 15 16:20:06 2021 +0000
@@ -6,8 +6,8 @@
             <yield/>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">0.3.7</token>
-    <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy1</token>
+    <token name="@TOOL_VERSION@">0.5.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="stdio">
         <stdio>
             <regex match="Aborted (core dumped)" source="stdout" level="fatal"/>
diff -r b21851ddcc79 -r 71730c177cdf test-data/test_bam_01_output_a.bam
Binary file test-data/test_bam_01_output_a.bam has changed
diff -r b21851ddcc79 -r 71730c177cdf test-data/test_bed_02_output_a__all.bed
--- a/test-data/test_bed_02_output_a__all.bed	Wed Sep 30 13:59:28 2020 +0000
+++ b/test-data/test_bed_02_output_a__all.bed	Thu Jul 15 16:20:06 2021 +0000
@@ -1,5 +1,5 @@
-chr1	100	10000	Fail
-chr2	100	10000	Fail
-chr3	100	10000	Fail
-chr4	8941700 8947200	Fail
-chr5	1	100000000	Fail
+chr1	100	10000	Unmap
+chr2	100	10000	Unmap
+chr3	100	10000	Unmap
+chr4	8941700 8947200	Unmap
+chr5	1	100000000	Unmap
diff -r b21851ddcc79 -r 71730c177cdf test-data/test_bed_02_output_a__only_fails.bed
--- a/test-data/test_bed_02_output_a__only_fails.bed	Wed Sep 30 13:59:28 2020 +0000
+++ b/test-data/test_bed_02_output_a__only_fails.bed	Thu Jul 15 16:20:06 2021 +0000
@@ -1,5 +1,5 @@
-chr1	100	10000
-chr2	100	10000
-chr3	100	10000
-chr4	8941700 8947200
-chr5	1	100000000
+chr1	100	10000	Unmap
+chr2	100	10000	Unmap
+chr3	100	10000	Unmap
+chr4	8941700 8947200	Unmap
+chr5	1	100000000	Unmap
diff -r b21851ddcc79 -r 71730c177cdf test-data/test_bigwig_01_output_a.bw
Binary file test-data/test_bigwig_01_output_a.bw has changed
diff -r b21851ddcc79 -r 71730c177cdf test-data/test_region.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_region.bed	Thu Jul 15 16:20:06 2021 +0000
@@ -0,0 +1,2 @@
+chr2	90000	990000	map_ratio=1.0000
+chr3	75000	975000	map_ratio=1.0000