diff crossmap_bed.xml @ 4:1e24dd91db95 draft

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

--- a/crossmap_bed.xml	Fri Oct 20 11:33:15 2017 -0400
+++ b/crossmap_bed.xml	Thu May 24 19:10:23 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="crossmap_bed" name="CrossMap BED" version="@WRAPPER_VERSION@-0">
+<tool id="crossmap_bed" name="CrossMap BED" version="@WRAPPER_VERSION@">
     <description>Convert genome coordinates or annotation files between genome assemblies</description>
     <macros>
         <import>macros.xml</import>
@@ -24,8 +24,7 @@
 #if $merge_unmapped_entries:
     > '${output_combined}'
 #else:
-    '${output_valid}'
-    && mv '${output_valid}.unmap' '${output_failed}'
+    output
 #end if
 
     ]]></command>
@@ -41,10 +40,10 @@
     </inputs>
 
     <outputs>
-        <data name="output_valid" format="bed" label="${tool.name} (valid only) on ${on_string}">
+        <data name="output_valid" format="bed" label="${tool.name} (valid only) on ${on_string}" from_work_dir="output">
             <filter>merge_unmapped_entries is False</filter>
         </data>
-        <data name="output_failed" format="bed" label="${tool.name} (failed only) on ${on_string}">
+        <data name="output_failed" format="bed" label="${tool.name} (failed only) on ${on_string}" from_work_dir="output.unmap">
             <filter>merge_unmapped_entries is False</filter>
         </data>
 
@@ -135,7 +134,6 @@
    skipped.
 7. If input region cannot be consecutively mapped target assembly, it will be split.
 8. \*.unmap file contains regions that cannot be unambiguously converted.
-
     ]]></help>
 
     <citations>