# HG changeset patch
# User yhoogstrate
# Date 1438757915 14400
# Node ID 0cae6e3273a85117c5e0c13d7e5a145a60d540d3
# Parent  9750f8c1d3cbe60ce371df2788bbae7f713c260b
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd

diff -r 9750f8c1d3cb -r 0cae6e3273a8 crossmap.xml
--- a/crossmap.xml	Tue Aug 04 09:43:29 2015 -0400
+++ b/crossmap.xml	Wed Aug 05 02:58:35 2015 -0400
@@ -7,7 +7,7 @@
     
     <stdio>
         <regex match="Usage: CrossMap.py" source="stdin" level="fatal"/>
-        <regex match="^@ " source="stdin" level="warning" />
+        <regex match=".*" source="both" level="log" description="tool progress"/>
     </stdio>
 
     <command>
@@ -35,7 +35,10 @@
                 "$multiple.seq_source.input_fasta"
             #end if 
             
-            $output
+            <!-- BED format does not write to the output file, but does write fails to stdout -->
+            > "$output"
+            
+            2>/dev/null
     </command>
 
     <inputs>
@@ -101,8 +104,8 @@
                             </param>
                         </when>
                         <when value="history">
-                            <param format="bed" name="input" type="data" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns." />
-                            <param type="data" name="input_chain" label="LiftOver chain file" />
+                            <param type="data" format="bed" name="input"       label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns." />
+                            <param type="data"              name="input_chain" label="LiftOver chain file" />
                         </when>
                 </conditional>
             </when>
@@ -243,7 +246,7 @@
     </inputs>
     
     <outputs>
-        <data format="text" name="output" label="${tool.name} on ${input.hid}: ${input.name}" />
+        <data format="text" name="output" label="${tool.name} on " />
     </outputs>
     
     <tests>