changeset 4:bbd9d5b629f2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622

--- a/crossmap_bigwig.xml	Fri Oct 20 11:31:34 2017 -0400
+++ b/crossmap_bigwig.xml	Thu May 24 19:08:23 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="crossmap_bw" name="CrossMap BigWig" version="@WRAPPER_VERSION@-0">
+<tool id="crossmap_bw" name="CrossMap BigWig" version="@WRAPPER_VERSION@">
     <description>Convert genome coordinates or annotation files between genome assemblies</description>
     <macros>
         <import>macros.xml</import>
@@ -11,9 +11,7 @@
 CrossMap.py bigwig
 '${chain_source.input_chain}'
 '${input}'
-'${output}'
-
-&& mv '${output}.bw' '${output}'
+output
     ]]></command>
 
     <inputs>
@@ -23,7 +21,7 @@
     </inputs>
 
     <outputs>
-        <data name="output" format="bigwig" label="${tool.name} on ${on_string}" />
+        <data name="output" format="bigwig" label="${tool.name} on ${on_string}" from_work_dir="output.bw" />
     </outputs>
 
     <tests>
@@ -54,7 +52,6 @@
 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>

--- a/macros.xml	Fri Oct 20 11:31:34 2017 -0400
+++ b/macros.xml	Thu May 24 19:08:23 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"/>