# HG changeset patch
# User iuc
# Date 1527203340 14400
# Node ID 454886ffaa4180ec6a9dfa0eb0e38a662f2e080f
# Parent  792bd038a59c2456bc94609510417209edf63057
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622

diff -r 792bd038a59c -r 454886ffaa41 crossmap_wig.xml
--- a/crossmap_wig.xml	Fri Oct 20 11:31:52 2017 -0400
+++ b/crossmap_wig.xml	Thu May 24 19:09:00 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="crossmap_wig" name="CrossMap Wig" version="@WRAPPER_VERSION@-0">
+<tool id="crossmap_wig" name="CrossMap Wig" version="@WRAPPER_VERSION@">
     <description>Convert genome coordinates or annotation files between genome assemblies</description>
     <macros>
         <import>macros.xml</import>
@@ -10,10 +10,7 @@
 CrossMap.py wig
 '${chain_source.input_chain}'
 '${input}'
-'${output}'
-
-&& mv '${output}.bw' '${output}'
-&& mv '${output}.sorted.bgr' '${output2}'
+output
     ]]></command>
 
     <inputs>
@@ -23,8 +20,8 @@
     </inputs>
 
     <outputs>
-        <data name="output" format="wig" label="${tool.name} on ${on_string}" />
-        <data name="output2" format="bedgraph" label="${tool.name} (bedgraph) on ${on_string}" />
+        <data name="output" format="bigwig" label="${tool.name} on ${on_string}" from_work_dir="output.bw" />
+        <data name="output2" format="bedgraph" label="${tool.name} (bedgraph) on ${on_string}" from_work_dir="output.sorted.bgr" />
     </outputs>
 
     <tests>
@@ -59,7 +56,6 @@
 wigToBigWig tool. We export files in bedGraph because it is usually much
 smaller than file in wiggle format, and more importantly, CrossMap
 internally transforms wiggle into bedGraph to increase running speed.
-
     ]]></help>
 
     <citations>
diff -r 792bd038a59c -r 454886ffaa41 macros.xml
--- a/macros.xml	Fri Oct 20 11:31:52 2017 -0400
+++ b/macros.xml	Thu May 24 19:09:00 2018 -0400
@@ -2,11 +2,11 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="0.2.5">crossmap</requirement>
+            <requirement type="package" version="0.2.7">crossmap</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@WRAPPER_VERSION@">0.2.5</token>
+    <token name="@WRAPPER_VERSION@">0.2.7</token>
     <xml name="stdio">
         <stdio>
             <regex match="Aborted (core dumped)" source="stdout" level="fatal"/>