# HG changeset patch
# User yhoogstrate
# Date 1400590496 14400
# Node ID 9fcffbe6c206fcc83b4c6cd1e620ffd4a60e1429
# Parent  cada2d2f0a7c057becc8617120876b82295e9d0b
Uploaded

diff -r cada2d2f0a7c -r 9fcffbe6c206 featurecounts.xml
--- a/featurecounts.xml	Wed Mar 26 09:12:30 2014 -0400
+++ b/featurecounts.xml	Tue May 20 08:54:56 2014 -0400
@@ -88,7 +88,11 @@
 					#end if
 					
 					; mv tmp.txt $output
+					
+					sed -e '1 s/$alignment_escaped/${alignment_name_escaped}/g' $output".summary" > tmp.txt
+					; mv tmp.txt $output".summary"
 				#end for
+				; mv $output".summary" $output_summary
 			#end if
 		#end if
 	</command>
@@ -186,6 +190,7 @@
 	
 	<outputs>
 		<data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
+		<data format="text" name="output_summary" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])} summary" />
 	</outputs>
 	
 	<help>
diff -r cada2d2f0a7c -r 9fcffbe6c206 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Mar 26 09:12:30 2014 -0400
+++ b/tool_dependencies.xml	Tue May 20 08:54:56 2014 -0400
@@ -22,7 +22,7 @@
 	<package name="featurecounts2bed" version="1.0.0">
 		<install version="1.0">
 			<actions>
-				<action type="shell_command">wget http://yhoogstrate@toolshed.dtls.nl/repos/yhoogstrate/featurecounts/raw-file/tip/featurecounts2bed.sh &amp;&amp; chmod 755 *.sh</action>
+				<action type="shell_command">wget http://testtoolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/raw-file/tip/featurecounts2bed.sh &amp;&amp; chmod 755 *.sh</action>
 				<action type="move_file">
 					<source>../featurecounts2bed.sh</source>
 					<destination>$INSTALL_DIR/bin</destination>