# HG changeset patch
# User yhoogstrate
# Date 1415889982 18000
# Node ID fae19d64e9de773f01c1c59adbc66133de8cc8b5
# Parent  31279ea9fbfaac3d8b8aade180dbc163d18f3b67
Uploaded

diff -r 31279ea9fbfa -r fae19d64e9de README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Thu Nov 13 09:46:22 2014 -0500
@@ -0,0 +1,53 @@
+FeatureCounts wrapper for Galaxy
+================================
+
+<http://bioinf.wehi.edu.au/featureCounts/>
+<http://subread.sourceforge.net/>
+
+FeatureCounts as part of the SUBREAD package is "a highly efficient and
+accurate read summarization program".
+
+Development
+-----------
+
+* Repository-Maintainer: Youri Hoogstrate
+
+* Repository-Development: <https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools>
+
+The tool wrapper has been written by Youri Hoogstrate from the Erasmus
+Medical Center (Rotterdam, Netherlands) on behalf of the Translational
+Research IT (TraIT) project:
+
+<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
+-------
+
+**featureCounts**:
+
+GPL (>=3)
+
+**featurecounts2bed**:
+
+GPL (>=3)
+
+**This wrapper**:
+
+    Copyright (C) 2013-2014  Youri Hoogstrate
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
diff -r 31279ea9fbfa -r fae19d64e9de featurecounts.xml
--- a/featurecounts.xml	Wed May 21 08:27:05 2014 -0400
+++ b/featurecounts.xml	Thu Nov 13 09:46:22 2014 -0500
@@ -1,10 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="featurecounts" name="featureCounts">
+<tool id="featurecounts" name="featureCounts" version="1.4.4.a">
 	<description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
 	<requirements>
 		<requirement type="package" version="1.4.4">featurecounts</requirement>
 		<requirement type="package" version="1.0.0">featurecounts2bed</requirement>
 	</requirements>
+	<version_command>featureCounts -v</version_command>
 	<command>
 		<!--
 			The following script is written in the "Cheetah" language:
@@ -226,7 +227,7 @@
 
 **featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.**
 
-*Liao Y1, Smyth GK, Shi W.* Bioinformatics. 2014 Apr 1;30(7):923-30.
+*Liao Y1, Smyth GK, Shi W.* - Bioinformatics. 2014 Apr 1;30(7):923-30.
 
 - http://www.ncbi.nlm.nih.gov/pubmed/24227677
 - http://dx.doi.org/10.1093/bioinformatics/btt656
@@ -242,13 +243,15 @@
 Contact
 -------
 
-The tool wrapper has been written by Youri Hoogstrate from the Erasmus Medical Center (Rotterdam, Netherlands) on behalf of the Translational Research IT (TraIT) project:
+The tool wrapper has been written by Youri Hoogstrate from the Erasmus
+Medical Center (Rotterdam, Netherlands) on behalf of the Translational
+Research IT (TraIT) project:
 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
 
-I want to thank the Marius van den Beek for his contribution to this wrapper.
-
-More tools by the Translational Research IT (TraIT) project can be found in the following repository:
-http://testtoolshed.g2.bx.psu.edu/
-
+More tools by the Translational Research IT (TraIT) project can be found
+in the following toolsheds:
+- http://toolshed.dtls.nl/
+- http://toolshed.g2.bx.psu.edu
+- http://testtoolshed.g2.bx.psu.edu/
 </help>
-</tool>
\ No newline at end of file
+</tool>
diff -r 31279ea9fbfa -r fae19d64e9de featurecounts2bed.sh
--- a/featurecounts2bed.sh	Wed May 21 08:27:05 2014 -0400
+++ b/featurecounts2bed.sh	Thu Nov 13 09:46:22 2014 -0500
@@ -1,5 +1,20 @@
 #!/bin/bash
 
+# featurecounts2bed - converts featureCounts output to BED format
+
+# Copyright 2013-2014, Youri Hoogstrate
+
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License at <http://www.gnu.org/licenses/> for
+# more details.
+
 # This tool has been written by Youri Hoogstrate from the Erasmus
 # Medical Center (Rotterdam, Netherlands) on behalf of the Translational
 # Research IT (TraIT) project:
@@ -9,6 +24,7 @@
 # found in the following repository:
 # http://toolshed.dtls.nl/
 
+
 exon_level="true"
 filename=""
 
diff -r 31279ea9fbfa -r fae19d64e9de tool_dependencies.xml
--- a/tool_dependencies.xml	Wed May 21 08:27:05 2014 -0400
+++ b/tool_dependencies.xml	Thu Nov 13 09:46:22 2014 -0500
@@ -6,30 +6,40 @@
 				<action type="shell_command">wget http://sourceforge.net/projects/subread/files/subread-1.4.4/subread-1.4.4-source.tar.gz &amp;&amp; tar -zxvf subread-1.4.4-source.tar.gz &amp;&amp; cd subread-1.4.4-source/src/ &amp;&amp; make -f Makefile.Linux &amp;&amp; cd ../../</action>
 				<action type="move_file">
 					<source>../subread-1.4.4-source/bin/featureCounts</source>
-					<destination>$INSTALL_DIR/bin</destination>
+					<destination>$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>
+					<!--<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!
+			Downloads and installs featureCounts; requires WGET, GNU AUTOTOOLS and TAR to be installed.
 		</readme>
 	</package>
 	
 	<package name="featurecounts2bed" version="1.0.0">
 		<install version="1.0">
 			<actions>
+				<action type="move_file">
+					<source>$REPOSITORY_INSTALL_DIR/featurecounts2bed.sh</source>
+					<destination>$INSTALL_DIR/bin/</destination>
+				</action>
+				<!--
+				Revert to the previous if the move command doesn't work
+				
 				<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>$INSTALL_DIR/bin</destination>
 				</action>
+				-->
+				<action type="chmod">
+					<file mode="555">$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>
 				</action>
 			</actions>
 		</install>