# HG changeset patch
# User yhoogstrate
# Date 1433157511 14400
# Node ID 63bd455ed299335e073e03237a752b5fb9786234
# Parent  ab0323782bb5211267cbb251f31ab38077468438
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty

diff -r ab0323782bb5 -r 63bd455ed299 README.rst
--- a/README.rst	Mon May 18 04:49:19 2015 -0400
+++ b/README.rst	Mon Jun 01 07:18:31 2015 -0400
@@ -21,10 +21,6 @@
 
 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
 
-More tools by the Translational Research IT (TraIT) project can be found in the following repository:
-
-http://toolshed.dtls.nl/
-
 License
 -------
 
diff -r ab0323782bb5 -r 63bd455ed299 featurecounts.xml
--- a/featurecounts.xml	Mon May 18 04:49:19 2015 -0400
+++ b/featurecounts.xml	Mon Jun 01 07:18:31 2015 -0400
@@ -39,7 +39,7 @@
 					#end if
 					
 					-o "$output"
-					-T $threads
+					-T \${GALAXY_SLOTS:-2}
 					
 					#if $extended_parameters.parameters == "extended"
 						-t $extended_parameters.gff_feature_type
@@ -148,8 +148,6 @@
 			<option value="bed">BED format (line per exon): chr "\t" start "\t" stop "\t" description "\t" readcount (tab-delimited)</option>
 		</param>
 		
-		<param name="threads" type="integer" value="2" min="1" label="Number of the CPU threads. Higher numbers only make sense with a higher number of samples." />
-		
 		<conditional name="extended_parameters">
 			<param name="parameters" type="select" label="featureCounts parameters" help="For more advanced featureCounts settings.">
 				<option value="default">Default settings</option>
diff -r ab0323782bb5 -r 63bd455ed299 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon May 18 04:49:19 2015 -0400
+++ b/tool_dependencies.xml	Mon Jun 01 07:18:31 2015 -0400
@@ -1,22 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
 	<package name="featurecounts" version="1.4.6.p1">
-		<install version="1.0">
-			<actions>
-				<action type="shell_command">wget http://garr.dl.sourceforge.net/project/subread/subread-1.4.6-p1/subread-1.4.6-p1-source.tar.gz &amp;&amp; tar -zxvf subread-1.4.6-p1-source.tar.gz &amp;&amp; cd subread-1.4.6-p1-source/src/ &amp;&amp; make -f Makefile.Linux &amp;&amp; cd ../../</action>
-				<action type="move_file">
-					<source>../subread-1.4.6-p1-source/bin/featureCounts</source>
-					<destination>$INSTALL_DIR/bin/</destination>
-				</action>
-				<action type="set_environment">
-					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-					<!--<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>-->
-				</action>
-			</actions>
-		</install>
-		<readme>
-			Downloads and installs featureCounts; requires WGET, GNU AUTOTOOLS and TAR to be installed.
-		</readme>
+		<repository changeset_revision="a4c247fdd71b" name="package_featurecounts_1_4_6" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" />
 	</package>
 	
 	<package name="featurecounts2bed" version="1.0.0">
@@ -27,8 +12,8 @@
 					<file mode="755">$INSTALL_DIR/bin/featurecounts2bed.sh</file>
 				</action>
 				<action type="set_environment">
-					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-					<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+					<environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+					<environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
 				</action>
 			</actions>
 		</install>