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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
author yhoogstrate
date Mon, 18 May 2015 04:49:19 -0400
parents
children 63bd455ed299
files README.rst featurecounts.xml featurecounts2bed.sh test-data/featureCounts_guide.gff test-data/featureCounts_input1.bam test-data/featureCounts_input2.bam test-data/output.tab test-data/output_summary.tab tool-data/gene_sets.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml
diffstat 11 files changed, 1196 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Mon May 18 04:49:19 2015 -0400
@@ -0,0 +1,59 @@
+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-Developers: Youri Hoogstrate, Marius van den Beek
+
+* 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/>.
+
+Acknowledgements
+----------------
+
+I would like to thank Marius van den Beek for his contributions to this project.
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/featurecounts.xml	Mon May 18 04:49:19 2015 -0400
@@ -0,0 +1,281 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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="1.4.6.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?
+		#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)
+			#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
+				featureCounts
+					-a 
+					#if $reference_gene_sets_source.source_select == "indexed_filtered"
+						"$reference_gene_sets_source.reference_gene_sets"
+					#else if $reference_gene_sets_source.source_select == "indexed_all"
+						"$reference_gene_sets_source.reference_gene_sets"
+					#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] ), $__app__.tool_data_tables[ 'gene_sets' ].get_fields() )[0][2] }"
+					#end if
+					
+					-o "$output"
+					-T $threads
+					
+					#if $extended_parameters.parameters == "extended"
+						-t $extended_parameters.gff_feature_type
+						-g $extended_parameters.gff_feature_attribute
+						$extended_parameters.summarization_level
+						$extended_parameters.contribute_to_multiple_features
+						$extended_parameters.protocol
+						$extended_parameters.multimapping_counts
+						-Q $extended_parameters.mapping_quality
+						$extended_parameters.fragment_counting
+						$extended_parameters.check_distance
+						-d $extended_parameters.minimum_fragment_length
+						-D $extended_parameters.maximum_fragment_length
+						$extended_parameters.only_both_ends
+						$extended_parameters.exclude_chimerics
+						$extended_parameters.namesort
+					#end if
+					
+					#for $alignment in $alignments
+						 ${alignment}
+					#end for
+					
+					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 $output tmp.txt
+					; egrep -v "^#" tmp.txt > tmp2.txt
+					; cut -f 1,$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 $output tmp.txt
+					; egrep -v "^#" tmp.txt | cut -f 1,$columns > $output
+				#end if
+				
+				## For every alignment, replace its filename for: "hid: sample name"
+				#for $alignment in $alignments
+					#set $alignment_escaped = str($alignment).replace('/', '\/').replace('.', '\.')
+					#set $alignment_name_escaped = str(alignment.hid)+": "+str($alignment.name).replace('\t',' ').replace('\\','\\\\').replace("'","\\'").replace('/','\/')
+					
+					#if $format.value == "tabdel_default" or $format.value == "tabdel_short"
+						; sed -e '1 s/$alignment_escaped/${alignment_name_escaped}/g' $output > tmp.txt
+					#elif $format.value == "bed":
+						; featurecounts2bed.sh -f "$output" > tmp.txt
+					#else
+						; sed -e '1,2 s/$alignment_escaped/${alignment_name_escaped}/g' $output > tmp.txt
+					#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>
+	
+	<inputs>
+		<param name="alignments" type="data" format="bam,sam" label="Alignment file" help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files in the series must be in THE SAME format." multiple="true" />
+		
+		<!-- Find out how to access the the GTF/GFF file(s) -->
+		<conditional name="reference_gene_sets_source">
+			<param name="source_select" type="select" label="GFF/GTF Source">
+				<option value="indexed_filtered">Use a built-in index (which fits your reference)</option>
+				<option value="history">Use reference from the history</option>
+				<option value="indexed_all">Use a built-in index (entire list) - avoid this option if possible; only useful if you design a workflow</option>
+				<option value="attribute">Use a built-in index based on the 'metadata.dbkey' attribute; ideal in workflows</option>
+			</param>
+			<when value="indexed_filtered">
+				<param name="reference_gene_sets" type="select" label="Reference Gene Sets used during alignment (GFF/GTF)" >
+					<options from_data_table="gene_sets"><!-- replaces 'from_file="gene_sets"' - more strict -->
+						<column name="name"  index="0"/>
+						<column name="dbkey" index="1"/>
+						<column name="value" index="2"/>
+						<filter type="data_meta" ref="alignments" multiple="false" key="dbkey" column="1" />
+						<validator type="no_options" message="No indexes are available for the selected input dataset" />
+					</options>
+				</param>
+			</when>
+			<when value="history">
+				<param name="reference_gene_sets" format="gff" type="data" label="Gene annotation file" help="The program assumes that the provided annotation file is in GTF format. Make sure that the gene annotation file corresponds to the same reference genome as used for the alignment." />
+			</when>
+			<when value="indexed_all">
+				<param name="reference_gene_sets" type="select" label="Reference Gene Sets used during alignment (GFF/GTF)" >
+					<options from_data_table="gene_sets"><!-- replaces 'from_file="gene_sets"' - more strict -->
+						<column name="name"  index="0"/>
+						<column name="dbkey" index="1"/>
+						<column name="value" index="2"/>
+						<validator type="no_options" message="No indexes are available for the selected input dataset" />
+					</options>
+				</param>
+			</when>
+			<when value="attribute">
+				<!-- Do nothing, determine GTF/GFF file at runtime -->
+			</when>
+		</conditional>
+		
+		<param name="format" type="select" label="Output format">
+			<option value="complex">featureCounts 1.4.0+ default (extensive; complex)</option>
+			<option value="tabdel_default" selected="true">Gene-name "\t" gene-count "\t" gene-length (tab-delimited)</option>
+			<option value="tabdel_short">Gene-name "\t" gene-count (tab-delimited)</option>
+			<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>
+				<option value="extended">Extended settings</option>
+			</param>
+			<when value="default">
+			</when>
+			<when value="extended">
+				<param name="gff_feature_type" type="text" value="exon" label="GFF feature type filter" help="Specify the feature type. Only rows which have the matched matched feature type in the provided GTF annotation file will be included for read counting. `exon' by default." />
+				
+				<param name="gff_feature_attribute" type="text" value="gene_id" label="GFF gene identifier" help="Specify the attribute type used to group features (eg. exons) into meta-features (eg. genes), when GTF annotation is provided. `gene_id' by default. This attribute type is usually the gene identifier. This argument is useful for the meta-feature level summarization." />
+				
+				<param name ="summarization_level" type="boolean" truevalue=" -f" falsevalue="" label="On feature level" help="If specified, read summarization will be performed at the feature level. By default (-f is not specified), the read summarization is performed at the meta-feature level." />
+				
+				<param name ="contribute_to_multiple_features" type="boolean" truevalue=" -O" falsevalue="" label="Allow read to contribute to multiple features" help="If specified, reads (or fragments if -p is specified) will be allowed to be assigned to more than one matched meta- feature (or matched feature if -f is specified)" />
+				
+				<param name="protocol" type="select" label="Strand specific protocol" help="Indicate if strand-specific read counting should be performed. It has three possible values: 0 (unstranded), 1 (stranded) and 2 (reversely stranded). 0 by default.">
+					<option value=" -s 0" selected="true">Unstranded</option>
+					<option value=" -s 1">Stranded (forwards)</option>
+					<option value=" -s 2">Stranded (reverse)</option>
+				</param>
+				
+				<param name="multimapping_counts" type="boolean" truevalue=" -M" falsevalue="" label="Count multi-mapping reads/fragments" help="If specified, multi-mapping reads/fragments will be counted (ie. a multi-mapping read will be counted up to N times if it has N reported mapping locations). The program uses the `NH' tag to find multi-mapping reads." />
+				
+				<param name="mapping_quality" type="integer" value="0" label="Minimum read quality" help="The minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 0 by default." />
+				
+				<param name="fragment_counting" type="boolean" truevalue=" -p" falsevalue="" label="PE: Count fragments instead of reads" help="Paired-end specific: If specified, fragments (or templates) will be counted instead of reads. The two reads from the same fragment must be adjacent to each other in the provided SAM/BAM file. If SAM/BAM input does not meet this requirement, the -S (sorting) option should be provided as well." />
+				
+				<param name="check_distance" type="boolean" truevalue=" -P" falsevalue="" label="PE: Check paired-end distance" help="Paired-end specific: If specified, paired-end distance will be checked when assigning fragments to meta-features or features. This option is only applicable when -p (Count fragments instead of reads) is specified. The distance thresholds should be specified using -d and -D (minimum and maximum fragment/template length) options." />
+				
+				<param name="minimum_fragment_length" type="integer" value="50" label="PE: Minimum fragment/template length." />
+				<param name="maximum_fragment_length" type="integer" value="600" label="PE: Maximum fragment/template length." />
+				
+				<param name="only_both_ends" type="boolean" truevalue=" -B" falsevalue="" label="PE: only allow fragments with both reads aligned"  help="Paired-end specific: If specified, only fragments that have both ends successfully aligned will be considered for summarization. This option is only applicable for paired-end reads." />
+				
+				<param name="exclude_chimerics" type="boolean" truevalue=" -C" falsevalue="" label="PE: Exclude chimeric fragments"  help="Paired-end specific: If specified, the chimeric fragments (those fragments that have their two ends aligned to different chromosomes) will NOT be included for summarization. This option is only applicable for paired-end read data." />
+				
+				<param name="namesort" type="boolean" truevalue=" -S" falsevalue="" label="PE: Name-sort reads (slow!)"  help="Paired-end specific: If specified, the program will reorder input reads according to their names and make reads from the same pair be adjacent to each other. This option should be provided when reads from the same pair are not adjacent to each other in input SAM/BAM files (for instance sorting reads by chromosomal locations could decouple reads from the same pair)." />
+			</when>
+		</conditional>
+	</inputs>
+	
+	<outputs>
+		<data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
+		<data format="tabular" name="output_summary" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])} summary" />
+	</outputs>
+	
+	<tests>
+		<test>
+			<param name="alignments" value="featureCounts_input1.bam,featureCounts_input2.bam" ftype="bam" />
+			<param name="source_select" value="history" />
+			<param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
+			<output name="output" file="output.tab"/>
+			<output name="output_summary" file="output_summary.tab"/>
+		</test>
+	</tests>
+	
+	<help>
+featureCounts
+#############
+
+Overview
+--------
+FeatureCounts is a light-weight read counting program written entirely in the C programming language. It can be used to count both gDNA-seq and RNA-seq reads for genomic features in in SAM/BAM files.
+It has a variety of advanced parameters but its major strength is its outstanding performance: analysis of a 10GB SE BAM file takes about 7 minutes on a single average CPU (Homo Sapiens genome) [1].
+
+Input formats
+-------------
+Alignments should be provided in either:
+
+- SAM format, http://samtools.sourceforge.net/samtools.shtml#5
+- BAM format
+
+Gene regions should be provided in the GFF/GTF format:
+
+- http://genome.ucsc.edu/FAQ/FAQformat.html#format3
+- http://www.ensembl.org/info/website/upload/gff.html
+
+Installation
+------------
+
+1. Make sure you have proper GFF/GTF files (corresponding to your reference genome used for the aligment) uploaded to your history.
+
+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
+
+License
+-------
+
+**featureCounts / subread package**:
+
+- GNU General Public License version 3.0 (GPLv3)
+
+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:
+
+http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
+
+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/
+
+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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/featurecounts2bed.sh	Mon May 18 04:49:19 2015 -0400
@@ -0,0 +1,78 @@
+#!/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:
+# 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/
+
+
+exon_level="true"
+filename=""
+
+# Parse parameters
+while getopts e:f: option
+do
+	case "${option}"
+	in
+		e) exon_level=${OPTARG};;
+		f) filename=$OPTARG;;
+	esac
+done
+
+# Convert the file
+if [ $filename == "" ]; then
+	echo "Usage:"
+	echo "  -e [true, false]   true = entry for every exon; false = line for genes first exon"
+	echo "  -f                 FILENAME from featureCounts"
+else
+	while read line; do
+		first=${line:0:1}
+		if [ $first != "#" ]; then
+			columns=($line)
+			uid=${columns[@]:0:1}
+			if [ $uid != "Geneid" ]; then
+				chr=${columns[@]:1:1}
+				start=${columns[@]:2:1}
+				stop=${columns[@]:3:1}
+				direction=${columns[@]:4:1}
+				length=${columns[@]:5:1}
+				count=${columns[@]:6:1}
+				
+				chr_splitted=($(echo $chr | tr ";" "\n"))
+				start_splitted=($(echo $start | tr ";" "\n"))
+				stop_splitted=($(echo $stop | tr ";" "\n"))
+				strand_splitted=($(echo $direction | tr ";" "\n"))
+				
+				if [ $exon_level == "true" ]; then
+					n=${#chr_splitted[@]}
+				else
+					n=1
+				fi
+				
+				for (( i=0; i<$n; i++ ))
+				do
+					echo ${chr_splitted[@]:$i:1}"	"${start_splitted[@]:$i:1}"	"${stop_splitted[@]:$i:1}"	"$uid" ("$((${stop_splitted[@]:$i:1}-${start_splitted[@]:$i:1}))"/"$length"nt)	"$count"	"${strand_splitted[@]:$i:1}
+				done
+			fi
+		fi
+	done < $filename
+fi
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/featureCounts_guide.gff	Mon May 18 04:49:19 2015 -0400
@@ -0,0 +1,680 @@
+X	FlyBase	exon	30948	31447	.	+	.	ID=FBti0062706;gene_id=left
+X	FlyBase	exon	32172	32671	.	+	.	ID=FBti0062706;gene_id=right
+X	FlyBase	exon	51312	51811	.	+	.	ID=FBti0062715;gene_id=left
+X	FlyBase	exon	52318	52817	.	+	.	ID=FBti0062715;gene_id=right
+X	FlyBase	exon	53883	54382	.	-	.	ID=FBti0062719;gene_id=left
+X	FlyBase	exon	55280	55779	.	-	.	ID=FBti0062719;gene_id=right
+X	FlyBase	exon	64215	64714	.	+	.	ID=FBti0062738;gene_id=left
+X	FlyBase	exon	65335	65834	.	+	.	ID=FBti0062738;gene_id=right
+X	FlyBase	exon	77479	77978	.	-	.	ID=FBti0063571;gene_id=left
+X	FlyBase	exon	78341	78840	.	-	.	ID=FBti0063571;gene_id=right
+X	FlyBase	exon	79405	79904	.	-	.	ID=FBti0063569;gene_id=left
+X	FlyBase	exon	80154	80653	.	-	.	ID=FBti0063569;gene_id=right
+X	FlyBase	exon	82402	82901	.	-	.	ID=FBti0063568;gene_id=left
+X	FlyBase	exon	83164	83663	.	-	.	ID=FBti0063568;gene_id=right
+X	FlyBase	exon	90012	90511	.	+	.	ID=FBti0062762;gene_id=left
+X	FlyBase	exon	90918	91417	.	+	.	ID=FBti0062762;gene_id=right
+X	FlyBase	exon	92326	92825	.	+	.	ID=FBti0062765;gene_id=left
+X	FlyBase	exon	93238	93737	.	+	.	ID=FBti0062765;gene_id=right
+X	FlyBase	exon	168410	168909	.	+	.	ID=FBti0062766;gene_id=left
+X	FlyBase	exon	169363	169862	.	+	.	ID=FBti0062766;gene_id=right
+X	FlyBase	exon	184346	184845	.	-	.	ID=FBti0062772;gene_id=left
+X	FlyBase	exon	185123	185622	.	-	.	ID=FBti0062772;gene_id=right
+X	FlyBase	exon	186159	186658	.	-	.	ID=FBti0019520;gene_id=left
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+X	FlyBase	exon	22271776	22272275	.	-	.	ID=FBti0061846;gene_id=left
+X	FlyBase	exon	22272465	22272964	.	-	.	ID=FBti0061846;gene_id=right
+X	FlyBase	exon	22276936	22277435	.	+	.	ID=FBti0061848;gene_id=left
+X	FlyBase	exon	22277765	22278264	.	+	.	ID=FBti0061848;gene_id=right
+X	FlyBase	exon	22283375	22283874	.	+	.	ID=FBti0062474;gene_id=left
+X	FlyBase	exon	22285380	22285879	.	+	.	ID=FBti0062474;gene_id=right
+X	FlyBase	exon	22289776	22290275	.	+	.	ID=FBti0062436;gene_id=left
+X	FlyBase	exon	22290575	22291074	.	+	.	ID=FBti0062436;gene_id=right
+X	FlyBase	exon	22326110	22326609	.	-	.	ID=FBti0062440;gene_id=left
+X	FlyBase	exon	22327885	22328384	.	-	.	ID=FBti0062440;gene_id=right
+X	FlyBase	exon	22336396	22336895	.	-	.	ID=FBti0062416;gene_id=left
+X	FlyBase	exon	22337937	22338436	.	-	.	ID=FBti0062416;gene_id=right
+X	FlyBase	exon	22339332	22339831	.	+	.	ID=FBti0061912;gene_id=left
+X	FlyBase	exon	22340231	22340730	.	+	.	ID=FBti0061912;gene_id=right
+X	FlyBase	exon	22385377	22385876	.	+	.	ID=FBti0061942;gene_id=left
+X	FlyBase	exon	22386134	22386633	.	+	.	ID=FBti0061942;gene_id=right
+X	FlyBase	exon	22397699	22398198	.	+	.	ID=FBti0062347;gene_id=left
+X	FlyBase	exon	22405375	22405874	.	+	.	ID=FBti0062347;gene_id=right
+X	FlyBase	exon	22406838	22407337	.	+	.	ID=FBti0062442;gene_id=left
+X	FlyBase	exon	22408770	22409269	.	+	.	ID=FBti0062442;gene_id=right
+X	FlyBase	exon	22412656	22413155	.	-	.	ID=FBti0061946;gene_id=left
+X	FlyBase	exon	22413523	22414022	.	-	.	ID=FBti0061946;gene_id=right
Binary file test-data/featureCounts_input1.bam has changed
Binary file test-data/featureCounts_input2.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.tab	Mon May 18 04:49:19 2015 -0400
@@ -0,0 +1,3 @@
+Geneid	1: featureCounts_input1.bam	2: featureCounts_input2.bam	Length
+left	92	72	170000
+right	66	63	170000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_summary.tab	Mon May 18 04:49:19 2015 -0400
@@ -0,0 +1,12 @@
+Status	1: featureCounts_input1.bam	2: featureCounts_input2.bam
+Assigned	158	135
+Unassigned_Ambiguity	0	0
+Unassigned_MultiMapping	0	0
+Unassigned_NoFeatures	6078	6344
+Unassigned_Unmapped	0	0
+Unassigned_MappingQuality	0	0
+Unassigned_FragementLength	0	0
+Unassigned_Chimera	0	0
+Unassigned_Secondary	0	0
+Unassigned_Nonjunction	0	0
+Unassigned_Duplicate	0	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/gene_sets.loc.sample	Mon May 18 04:49:19 2015 -0400
@@ -0,0 +1,39 @@
+# This is a sample file distributed with Galaxy that enables tools
+# to use gene/exon annotations in the GFF/GTF format. You will need
+# to add all the gene set annotations in this configuration file.
+# Because of this file, galaxy tools are able to access gene annotations
+# provided as GFF / GTF files by selecting on:
+# - Priorty (defined by the order in the file)
+# - Provider
+# - dbkey (reference genome id)
+# 
+# The gene_sets.loc file syntax is:
+# <name/UID> <dbkey> <path> <provider> <URL/reference*>
+#  *optional
+# 
+# Please ensure maximally one TAB (\t) between two columns!
+# ---------------------------------------------------------
+# 
+# In case you have TWO or MORE providers PER dbkey, the one mentioned
+# first in the file, should have the "default" priority.
+#
+
+
+
+# [UCSC - UCSC Genes: knownGene]
+
+#hg19.UCSC knownGene (mm/'yy)	hg19	/depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf	ucsc	http://genome.ucsc.edu/
+#hg18.UCSC knownGene (mm/'yy)	hg18	/depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf	ucsc	http://genome.ucsc.edu/
+
+
+
+# [RefSeq Genes: RefGene]
+# link: ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene/
+
+
+
+# [ Ensembl]
+# link: http://www.ensembl.org/info/data/ftp/index.html
+
+#Homo_sapiens.GRCh37.74	hg19	/depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf	ensembl	ftp://ftp.ensembl.org/pub/release-74/gtf/homo_sapiens/Homo_sapiens.GRCh37.74.gtf.gz
+#Homo_sapiens.NCBI36.54	hg18	/depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf	ensembl	ftp://ftp.ensembl.org/pub/release-54/gtf/homo_sapiens/Homo_sapiens.NCBI36.54.gtf.gz
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Mon May 18 04:49:19 2015 -0400
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Location of all GFF/GTF files -->
+    <table name="gene_sets" comment_char="#">
+        <columns>name, dbkey, value, provider, reference</columns>
+        <file path="tool-data/gene_sets.loc" />
+    </table>
+</tables>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon May 18 04:49:19 2015 -0400
@@ -0,0 +1,36 @@
+<?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>
+	</package>
+	
+	<package name="featurecounts2bed" version="1.0.0">
+		<install version="1.0">
+			<actions>
+				<action type="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/featurecounts2bed.sh $INSTALL_DIR/bin/</action>
+				<action type="chmod">
+					<file mode="755">$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>
+				</action>
+			</actions>
+		</install>
+	</package>
+</tool_dependency>