<tool id="cshl_princeton_fastx_barcode_splitter" version="1.1" name="Barcode Splitter" force_history_refresh="True">
	<description></description>
	<command interpreter="bash">
		fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "primary_$output.id" "$__new_file_path__" $input.extension --mismatches $mismatches --partial $partial 
		#if $refBarcodeLocation.barcodeLocation == "idxfile":
		  --idxfile $refBarcodeLocation.idxfile 
		#else: 
		  $refBarcodeLocation.EOL 
		#end if
		> $output
	</command>

	<inputs>
		<param format="txt" version="1.1" name="BARCODE" type="data" label="Barcodes to use" />
		<param format="fasta,fastqsanger,fastqsolexa,fastqillumina" version="1.1" name="input" type="data" label="Library to split" />

		<conditional name="refBarcodeLocation">
			<param version="1.1" name="barcodeLocation" type="select" label="Barcodes found at">
				<option value="bol">Start of sequence (5' end)</option>
				<option value="eol">End of sequence (3' end)</option>
				<option value="idxfile">Separate index file</option>
			</param>
			<when value="bol">
				<param version="1.1" name="EOL" type="hidden" value="--bol" />
			</when>
			<when value="eol">
				<param version="1.1" name="EOL" type="hidden" value="--eol" />
			</when>
			<when value="idxfile">
				<param version="1.1" name="idxfile" type="data" format="fasta,fastq,fastqsanger" label="Select index read file" />
			</when>
		</conditional>

		<param version="1.1" name="mismatches" type="integer" size="3" value="0" label="Number of allowed mismatches" />
		
		<param version="1.1" name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" />
	
	</inputs>
	
	<tests>
		<test>
			<!-- Split a FASTQ file -->
			<param version="1.1" name="BARCODE" value="fastx_barcode_splitter1.txt" />
			<param version="1.1" name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
			<param version="1.1" name="EOL" value="Start of sequence (5' end)" />
			<param version="1.1" name="mismatches" value="2" />
			<param version="1.1" name="partial" value="0" />
			<output version="1.1" name="output" file="fastx_barcode_splitter1.out" />
		</test>
	</tests>

	<outputs>
		<data version="1.1" format="html" name="output" />
	</outputs>
<help>

**What it does**

This tool splits a FASTQ or FASTA file into several files, using barcodes as the split criteria.

--------

**Barcode file Format**

Barcode files are simple text files.
Each line should contain an identifier (descriptive name for the barcode), and the barcode itself (A/C/G/T), separated by a TAB character.
Example::

    #This line is a comment (starts with a 'number' sign)
    BC1	GATCT
    BC2	ATCGT
    BC3	GTGAT
    BC4 TGTCT
    
For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name).
Sequences matching the barcode will be stored in the appropriate file.

One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored.

The output of this tool is an HTML file, displaying the split counts and the file names.
In addition, each fastq file produced will be loaded into the galaxy history automatically.


------

This tool is based on `FASTX-toolkit`__ by Assaf Gordon.

 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
 
</help>
<!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
</tool>