# HG changeset patch
# User yhoogstrate
# Date 1393590406 18000
# Node ID c55c0c51b63466fc6701f8c25bc3327d48c557d4
# Parent  4850787ee1d9438ddce0993fd348dd9219cbd42d
Uploaded

diff -r 4850787ee1d9 -r c55c0c51b634 featurecounts_valid_gff.xml
--- a/featurecounts_valid_gff.xml	Mon Feb 24 08:19:34 2014 -0500
+++ b/featurecounts_valid_gff.xml	Fri Feb 28 07:26:46 2014 -0500
@@ -76,6 +76,20 @@
 					; cp $output tmp.txt
 					; egrep -v "^#" tmp.txt | cut -f 1,7 > $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 == "tabdel_default" or $format.value == "tabdel_default" or $format == "tabdel_short" or $format.value == "tabdel_short"
+						; sed -e '1 s/$alignment_escaped/${alignment_name_escaped}/g' $output > tmp.txt
+					#else
+						; sed -e '1,2 s/$alignment_escaped/${alignment_name_escaped}/g' $output > tmp.txt
+					#end if
+					
+					; mv tmp.txt $output
+				#end for
 			#end if
 		#end if
 	</command>
@@ -102,6 +116,9 @@
 					</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 annotaiton 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 -->
@@ -112,9 +129,6 @@
 					</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 annotaiton file corresponds to the same reference genome as used for the alignment." />
-			</when>
 			<when value="attribute">
 				<!-- Do nothing, determine GTF/GFF file at runtime -->
 			</when>
@@ -176,7 +190,6 @@
 	
 	<help>
 featureCounts-valid-gff::
-
 **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.
@@ -192,8 +205,9 @@
 * http://genome.ucsc.edu/FAQ/FAQformat.html#format3
 * http://www.ensembl.org/info/website/upload/gff.html
 
-FeatureCounts is only able to handle the UCSC variant. Therefore the project was forked to "featureCounts-valid-gff", able to handle both.
-Whis wrapper wraps the fork, such that it is independent of the GFF/GTF variant.
+FeatureCounts is only able to handle the UCSC GFF/GTF variant. Therefore the project was forked to "featureCounts-valid-gff", able to handle both.
+Whis wrapper wraps the fork, such that it is independent of the GFF/GTF variant. The URL of the fork is:
+https://code.google.com/p/featurecounts-valid-gff/
 
 **Input formats**
 
@@ -225,6 +239,8 @@
 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 as well.
+
 More tools by the Translational Research IT (TraIT) project can be found in the following repository:
 http://toolshed.nbic.nl/