Mercurial > repos > yhoogstrate > featurecounts

changeset 1:9fcffbe6c206 draft

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Uploaded
author yhoogstrate
date Tue, 20 May 2014 08:54:56 -0400
parents cada2d2f0a7c
children 8c70c248576e
files featurecounts.xml tool_dependencies.xml
diffstat 2 files changed, 6 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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>
--- 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>