view fastx_barcode_splitter_single.xml @ 0:bc23f6946bb8 default tip

Alternative barcode splitters that move selected results to the users history.

<tool id="cshl_fastx_barcode_splitter_single" name="Barcode Splitter (Single)">
	<description></description>
	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
	<command interpreter="python">fastx_barcode_splitter_single_galaxy_wrapper.py 
           $matched_output 
           $unmatched_output
           "$input.ext" 
           --barcodes='$barcode'
           $input "$input.name"
            --mismatches $mismatches --partial $partial $EOL 
        </command>

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

		<param name="EOL" type="select" label="Barcodes found at">
			<option value="--bol">Start of sequence (5' end)</option>
			<option value="--eol">End of sequence (3' end)</option>
		</param>

		<param name="mismatches" type="integer" size="3" value="2" label="Number of allowed mismatches" />
		
		<param name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" />

    <param name="barcode" type="text" label="Barcode to extract" />

    <!-- 
                <param name="barcodes" type="select" multiple="true" label="Select barcodes to add as new datasets to history">
		    <options from_dataset="BARCODE">
    			<column name="name" index="0"/>
    			<column name="value" index="0"/>
                        <filter type="unique_value" name="unq_bc" column="0" />
                        <filter type="add_value" name="unmatched" value="unmatched"/>
		    </options>
                </param>
    -->
	</inputs>

	<outputs>
		<data format_source="input" name="matched_output" label="Barcode Splitter on ${input.name} (Matching sequences)" />
    <data format_source="input" name="unmatched_output" label="Barcode Splitter on ${input.name} (Unmatched sequences)" />
	</outputs>
	
	<tests>
	</tests>

<help>

**What it does**

This tool splits a Solexa library (FASTQ file) or a regular FASTA file into two files using a barcode as the split criteria.

--------

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.

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

</help>
</tool>
<!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon ([e-mail]) -->