# HG changeset patch
# User davidvanzessen
# Date 1482332862 18000
# Node ID cbce7f35f8b0a5557a44f7687f13a3ee9ebaa366
# Parent  cb08a27e5fc28a88594b77744a6c7fed77259159
Uploaded

diff -r cb08a27e5fc2 -r cbce7f35f8b0 demultiplex.xml
--- a/demultiplex.xml	Mon Aug 29 05:44:57 2016 -0400
+++ b/demultiplex.xml	Wed Dec 21 10:07:42 2016 -0500
@@ -340,10 +340,55 @@
 		<data format="html" name="out_file" />
 	</outputs>
 	<help>
-- 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.
-		
+**References**
+
+This tool makes use of the following freely available tools:
+
+- Sequences which are missing a gene region (FR1/CDR1 etc) in the analysed region are excluded
+- Sequences containing an ambiguous base in the analysed region are excluded
+- All other filtering/analysis is based on the analysed region
+
+**Input files**
+
+This tool uses .sff  files as input files. 
+
+.. class:: infomark
+
+Note: Files can be uploaded by using “get data” and “upload file”. No “type” or “Genome” have to be selected. Special characters should be prevented in the file names of the uploaded samples as these can give errors when running the immune repertoire pipeline. Underscores are allowed in the file names.
+
+**File to split**
+
+Please select here the file you would like to demultiplex.
+
+**Barcodes**
+
+*ID*: Please provide here for each sample to demultiplex, a sample name (consistent only out of letters, numbers and underscores)
+
+*Mid*: select the correct multiplex identifier (MID) tag that this sample is linked to. These MIDs tags originate from the Roche 454 (TCB No. 005-2009). You can either choose to search for the MID sequence at in the 5’to 3’prime direction or the reverse complement.
+
+*How many nucleotides to trim from the start*: indicate the number nucleotides that you would like to trim from the 5’ side of your read
+
+*How many nucleotides to trim from the end*: indicate the number nucleotides that you would like to trim from the 3’ side of your read
+
+*Insert Barcodes*: The insert barcodes button can be used to add more samples and their linked MID tags. 
+
+**Barcodes found at**
+
+Please select whether the barcodes (MID tags) can be found at the 5’end or the 3’end of the sequence.
+
+**Max. number of mismatches allowed**
+
+Please select the maximal number of mismatches allows in the MID tag.
+
+**Allow partial overlap of barcodes**
+
+Select the amount of overlap that is allowed between different barcodes. 
+
+**Execute**
+
+Upon pressing execute a new analysis is added to your history (right side of the page). Initially this analysis will be grey, after initiating the analysis colour of the analysis in the history will change to yellow. When the analysis is finished it will turn green in the history. Now the analysis can be opened by clicking on the eye icon on the analysis of interest. When an analysis turns red an error has occurred when running the analysis. If you click on the analysis title additional information can be found on the analysis. In addition a bug icon appears. Here more information on the error can be found.
+
+
+
 	</help>
 </tool>