# HG changeset patch
# User iuc
# Date 1568244578 14400
# Node ID 5051467dc96a53d9535b131240d1bfe562d2ec04
# Parent  cb3557cabc7b0985610687cc455668cf1521e525
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"

diff -r cb3557cabc7b -r 5051467dc96a crossmap_bam.xml
--- a/crossmap_bam.xml	Thu May 24 19:10:46 2018 -0400
+++ b/crossmap_bam.xml	Wed Sep 11 19:29:38 2019 -0400
@@ -7,6 +7,9 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
+
+ln -s '${input}' ./input.bam &&
+
 CrossMap.py bam
 '${chain_source.input_chain}'
 $optional_tags
@@ -15,7 +18,7 @@
 -s $insert_size_stdev
 -t $insert_size_fold
 
-'${input}'
+./input.bam
 output
     ]]></command>
     <inputs>
@@ -27,7 +30,8 @@
 
         <param name="insert_size" argument="-m" type="float" value="200.0" label="Insert size" help="Average insert size of pair-end sequencing (bp)"/>
         <param name="insert_size_stdev" argument="-s" type="float" value="30.0" label="Insert size std. dev" help="Stanadard deviation of insert size"/>
-        <param name="insert_size_fold" argument="-t" type="float" value="3.0" label="Insert size std. dev foldchange" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean"/>
+        <param name="insert_size_fold" argument="-t" type="float" value="3.0" label="Insert size std. dev foldchange"
+            help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean"/>
     </inputs>
 
     <outputs>
diff -r cb3557cabc7b -r 5051467dc96a macros.xml
--- a/macros.xml	Thu May 24 19:10:46 2018 -0400
+++ b/macros.xml	Wed Sep 11 19:29:38 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 cb3557cabc7b -r 5051467dc96a test-data/test_bigwig_01_output_a.bw
Binary file test-data/test_bigwig_01_output_a.bw has changed
diff -r cb3557cabc7b -r 5051467dc96a test-data/test_vcf_01_output.vcf.unmap
--- a/test-data/test_vcf_01_output.vcf.unmap	Thu May 24 19:10:46 2018 -0400
+++ b/test-data/test_vcf_01_output.vcf.unmap	Wed Sep 11 19:29:38 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 cb3557cabc7b -r 5051467dc96a test-data/test_wig_01_output_a.bw
Binary file test-data/test_wig_01_output_a.bw has changed