# HG changeset patch
# User iuc
# Date 1568244561 14400
# Node ID 9d61d74f03a4d6f278e380161bd2c3478a201219
# Parent  9db73ff23c9f8db10d98d9b829b258f23d00aca3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"

diff -r 9db73ff23c9f -r 9d61d74f03a4 crossmap_vcf.xml
--- a/crossmap_vcf.xml	Thu May 24 19:09:50 2018 -0400
+++ b/crossmap_vcf.xml	Wed Sep 11 19:29:21 2019 -0400
@@ -7,7 +7,7 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
 
-    <command><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
 #set $input_file = str($seq_source.input)
 
 CrossMap.py vcf
@@ -77,7 +77,6 @@
                     <has_text text="#CHROM"/>
                     <has_text_matching expression="2.*?rs11449.*?PASS"/>
                     <has_text_matching expression="2.*?rs84825.*?PASS"/>
-                    <has_text_matching expression="2.*?rs84823.*?PASS"/>
                 </assert_contents>
             </output>
             <output name="output_unmapped" file="test_vcf_01_output.vcf.unmap"/>
diff -r 9db73ff23c9f -r 9d61d74f03a4 macros.xml
--- a/macros.xml	Thu May 24 19:09:50 2018 -0400
+++ b/macros.xml	Wed Sep 11 19:29:21 2019 -0400
@@ -2,11 +2,12 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="0.2.7">crossmap</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">crossmap</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@WRAPPER_VERSION@">0.2.7</token>
+    <token name="@TOOL_VERSION@">0.3.7</token>
+    <token name="@WRAPPER_VERSION@">@TOOL_VERSION@</token>
     <xml name="stdio">
         <stdio>
             <regex match="Aborted (core dumped)" source="stdout" level="fatal"/>
diff -r 9db73ff23c9f -r 9d61d74f03a4 test-data/test_bigwig_01_output_a.bw
Binary file test-data/test_bigwig_01_output_a.bw has changed
diff -r 9db73ff23c9f -r 9d61d74f03a4 test-data/test_vcf_01_output.vcf.unmap
--- a/test-data/test_vcf_01_output.vcf.unmap	Thu May 24 19:09:50 2018 -0400
+++ b/test-data/test_vcf_01_output.vcf.unmap	Wed Sep 11 19:29:21 2019 -0400
@@ -3,3 +3,4 @@
 ##FORMAT=<ID=GP,Number=G,Type=Float,Description="Genotype Probabilities">
 ##FORMAT=<ID=PL,Number=G,Type=Float,Description="Phred-scaled Genotype Likelihoods">
 #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)
diff -r 9db73ff23c9f -r 9d61d74f03a4 test-data/test_wig_01_output_a.bw
Binary file test-data/test_wig_01_output_a.bw has changed