diff crossmap_wig.xml @ 4:454886ffaa41 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622
author iuc
date Thu, 24 May 2018 19:09:00 -0400
parents 792bd038a59c
children b81b5d67bd3b
line wrap: on
line diff
--- 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>