# HG changeset patch
# User yhoogstrate
# Date 1426766896 14400
# Node ID 1a288d568ac15b2636653d5920237e5064fc82e8
# Parent  2312bedfe2a35f23bba173149e54d3296a2c2166
Uploaded

diff -r 2312bedfe2a3 -r 1a288d568ac1 README.rst
--- a/README.rst	Wed Nov 19 10:07:59 2014 -0500
+++ b/README.rst	Thu Mar 19 08:08:16 2015 -0400
@@ -11,6 +11,7 @@
 -----------
 
 * Repository-Maintainer: Youri Hoogstrate
+* Repository-Developers: Youri Hoogstrate, Marius van den Beek
 
 * Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools
 
@@ -51,3 +52,8 @@
 
     You should have received a copy of the GNU General Public License
     along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Acknowledgements
+----------------
+
+I would like to thank Marius van den Beek for his contributions to this project.
\ No newline at end of file
diff -r 2312bedfe2a3 -r 1a288d568ac1 featurecounts.xml
--- a/featurecounts.xml	Wed Nov 19 10:07:59 2014 -0500
+++ b/featurecounts.xml	Thu Mar 19 08:08:16 2015 -0400
@@ -1,22 +1,22 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="featurecounts" name="featureCounts" version="1.4.4.a">
+<tool id="featurecounts" name="featureCounts" version="1.4.6.p1">
 	<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="1.4.6.p1">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:
 			http://www.cheetahtemplate.org/docs/users_guide_html_multipage/contents.html
-		-->
+		*#
 		
-		<!-- Check 01: do the alignments have a dbkey and is the option set to using it?  -->
+		## Check 01: do the alignments have a dbkey and is the option set to using it?
 		#if $reference_gene_sets_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1
 			echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/gene_sets.loc' is configured properly!" >&amp;2
 		#else
-			<!-- Check 02: are all alignments from the same type (bam || sam)  -->
+			## Check 02: are all alignments from the same type (bam || sam)
 			#if len({ alignment.extension:True for alignment in $alignments }.keys()) != 1
 				echo "Either all files must be SAM or all files must be BAM, no mixture is allowed." >&amp;2
 			#else
@@ -29,12 +29,12 @@
 					#else if $reference_gene_sets_source.source_select == "history"
 						"$reference_gene_sets_source.reference_gene_sets"
 					#else
-						<!--
+						#*
 							This is a workaround to obtain the "genome.fa" file that
 							corresponds to the dbkey of the alignments.
 							Because this file is "calculated" during run-time, it can
 							be used in a workflow.
-						-->
+						*#
 						"${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'gene_sets' ].get_fields() )[0][2] }"
 					#end if
 					
@@ -64,15 +64,17 @@
 					
 					2>&amp;1
 				
+                                #set $columns = [str(i+7) for i, alignment in enumerate($alignments)]
+                                #set $columns=",".join($columns)
 				#if $format == "tabdel_default" or $format.value == "tabdel_default"
 					; cp $output tmp.txt
 					; egrep -v "^#" tmp.txt > tmp2.txt
-					; cut -f 1,7 tmp2.txt > tmp_left.txt
+					; cut -f 1,$columns tmp2.txt > tmp_left.txt
 					; cut -f 6 tmp2.txt > tmp_right.txt
 					; paste tmp_left.txt tmp_right.txt > $output
 				#elif $format == "tabdel_short" or $format.value == "tabdel_short"
 					; cp $output tmp.txt
-					; egrep -v "^#" tmp.txt | cut -f 1,7 > $output
+					; egrep -v "^#" tmp.txt | cut -f 1,$columns > $output
 				#end if
 				
 				## For every alignment, replace its filename for: "hid: sample name"
@@ -191,9 +193,13 @@
 	
 	<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 $alignments ])} summary" />
+		<data format="tabular" name="output_summary" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])} summary" />
 	</outputs>
-	
+        
+        <tests>
+	    <test>
+            </test>
+        </tests>
 	<help>
 featureCounts
 #############
@@ -222,17 +228,6 @@
 
 2. Make sure that your gene_sets.loc is configured properly as data table. This is generally done by copying the right information into: tool_data_table_conf.xml. More info at:  https://wiki.galaxyproject.org/Admin/Tools/Data%20Tables
 
-References
-----------
-
-**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.
-
-- http://www.ncbi.nlm.nih.gov/pubmed/24227677
-- http://dx.doi.org/10.1093/bioinformatics/btt656
-
-
 License
 -------
 
@@ -257,5 +252,23 @@
 http://toolshed.g2.bx.psu.edu/
 
 http://testtoolshed.g2.bx.psu.edu/
+
+References
+----------
+**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.
+
+- http://www.ncbi.nlm.nih.gov/pubmed/24227677
+- http://dx.doi.org/10.1093/bioinformatics/btt656
+
+
+Acknowledgements
+----------------
+
+I would like to thank Marius van den Beek for his contributions to this project.
 </help>
+<citations>
+    <citation type="doi">10.1093/bioinformatics/btt656</citation>
+</citations>
 </tool>
diff -r 2312bedfe2a3 -r 1a288d568ac1 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Nov 19 10:07:59 2014 -0500
+++ b/tool_dependencies.xml	Thu Mar 19 08:08:16 2015 -0400
@@ -1,11 +1,11 @@
 <?xml version="1.0"?>
 <tool_dependency>
-	<package name="featurecounts" version="1.4.4">
+	<package name="featurecounts" version="1.4.6.p1">
 		<install version="1.0">
 			<actions>
-				<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="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-1.4.4-source/bin/featureCounts</source>
+					<source>../subread-1.4.6-p1-source/bin/featureCounts</source>
 					<destination>$INSTALL_DIR/bin/</destination>
 				</action>
 				<action type="set_environment">