# HG changeset patch
# User davidvanzessen
# Date 1448445774 18000
# Node ID 5a886d753c0a3171d59483585e3b38647e0e22fb
# Parent  7973dd7a39ab1eee443b80c73032b04cb9ebb30e
Uploaded

diff -r 7973dd7a39ab -r 5a886d753c0a demultiplex.xml
--- a/demultiplex.xml	Tue Nov 04 09:16:17 2014 -0500
+++ b/demultiplex.xml	Wed Nov 25 05:02:54 2015 -0500
@@ -4,7 +4,7 @@
 		<requirement type="package" version="0.0.13">fastx_toolkit</requirement>
 	</requirements>
 	<command interpreter="bash">
-		wrapper.sh $input $out_file $out_file.files_path $where $mismatches $partial $input.name
+		wrapper.sh "$input" "$out_file" "$out_file.files_path" "$where" "$mismatches" "$partial" "$input.name"
 		#for $i, $b in enumerate($barcodes)
             "$b.id"
             "$b.mid"
@@ -340,7 +340,7 @@
 		<data format="html" name="out_file" />
 	</outputs>
 	<help>
-- Splitting sff files into FASTQ, FASTA and (optional) trimmed FASTA files with a FASTQC report on the FASTQ file, this tool uses:
+- Splitting sff or fastq files into FASTQ, FASTA and (optional) trimmed FASTA files with a FASTQC report on the FASTQ file, this tool uses:
 - sff2fastq (https://github.com/indraniel/sff2fastq) to extract a fastq file.
 - fastx_barcode_splitter.pl (http://hannonlab.cshl.edu/fastx_toolkit/commandline.html) to demultiplex.
 - fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to provide analysis of the fastq files.
diff -r 7973dd7a39ab -r 5a886d753c0a wrapper.sh
--- a/wrapper.sh	Tue Nov 04 09:16:17 2014 -0500
+++ b/wrapper.sh	Wed Nov 25 05:02:54 2015 -0500
@@ -1,11 +1,11 @@
 #!/bin/bash
-input=$1
-output=$2 
-outDir=$3
-mkdir $outDir
-EOL=$4
-mismatches=$5
-partial=$6
+input="$1"
+output="$2"
+outDir="$3"
+mkdir "$outDir"
+EOL="$4"
+mismatches="$5"
+partial="$6"
 name=$(basename "$7")
 ext="${name##*.}"
 name="${name%.*}"
@@ -23,7 +23,7 @@
 	start_int=$((i+2))
 	end_int=$((i+3))
 	id="${!i}"
-	echo "$id"
+	echo "$id, ${start_int}, ${end_int}"
 	trim_start[$id]=${!start_int}
 	trim_end[$id]=${!end_int}
   echo -e "$id\t${!j}" >> $outDir/barcodes.txt