<tool id="stripBarcode" name="Strip 5' degenerate barcode">
  <description></description>
  <command interpreter="perl">
	/home/galaxy/tools/CTK/stripBarcode.pl -len $Len -format $InputFormat
	#if $LinkerStart.startRequired == "yes":
		--barcode-start-with $LinkerStart.startwith
	#end if
	#if $LinkerEnd.endRequired == "yes":
		--barcode-end-with $LinkerEnd.endwith
	#end if
	-v $input $output
  </command>

  <inputs>
        <param name="InputFormat" type="select" label="Input FASTA or FASTQ format?">
		<option value="fastq">FASTQ</option>
		<option value="fasta">FASTA</option>
	</param>
	<param format="fastq,fastq.gz" name="input" type="data" label="Input file that contains 5' degenerate barcodes (.gz file accepted)">
		<change_format>
			<when input="InputFormat" value="fasta" format="fasta,fasta.gz" />
		</change_format>
        </param>
   
	<param name="Len" type="integer" value="" label="Length of degenerate barcode (also include sample index)" />

	<conditional name="LinkerStart">
		<param name="startRequired" type="select" label="Filter sequences based on the starting nucleotides in the barcode">
		<option value="yes">Yes</option>
		<option value="no" selected="True">No</option>
		</param>
		<when value="yes">
			<param name="startwith" type="text" value="" label="Starting nucleotides (case sensitive)" />
		</when>
		<when value="no">
		</when>
	</conditional>
	
	<conditional name="LinkerEnd">
		<param name="endRequired"  type="select" label="Filter sequences based on the ending nucleotides in the barcode">
		<option value="yes">Yes</option>
		<option value="no" selected="True">No</option>
		</param>
		<when value="yes">
			<param name="endwith" type="text" value="" label="Ending nucleotides (case sensitive)" />
		</when>
		<when value="no">
		</when>
	</conditional>
  </inputs>

  <outputs>
	<data name="output" format="fastq" label="Strip 5' degenerate barcode on ${on_string}"> 
	</data>	
  </outputs>
  <help>

.. class:: infomark

**What this tool does**

The 5' degenerate barcode is used to distinguish PCR duplicates from bona fide unique tags mapped to the same coordinates. This tool will strip random barcode sequences and attach that in sequence ids.

It will take as input files in FASTQ format that contains 5' degenerate barcodes and output files in FASTQ format with barcodes removed and attached to sequence ids. 

If you have extra barcodes next to the degenerate barcode, include the barcode in the length.

Examples::

        >seq1
        ACGTATTTTTTT

will become::

        >seq1#ACGTA
        TTTTTTT

-----

**Filter sequences**

You can also filter your sequences based on the starting or ending nucleotides in the barcode, which is useful for quality control purposes or multiplex samples.
</help>
</tool>