Hello Philippe,

I won't lie to you, I don't what these barcodes are or what this tool
actually does. However I had a similar request internally a while ago
and at that time I hacked up a new barcode splitter tool that just
takes in one barcode and produces a fixed number of outputs that can
be used in workflows, I was told that it was working and useful at the
time. I have attached the tool and wrapper to this e-mail in case they
are likewise useful to you.

-John

------------------------------------------------
John Chilton
Senior Software Developer
University of Minnesota Supercomputing Institute
Office: 612-625-0917
Cell: 612-226-9223
Bitbucket: https://bitbucket.org/jmchilton
Github: https://github.com/jmchilton
Web: http://jmchilton.net

On Sun, Oct 21, 2012 at 6:14 PM, Philipe Moncuquet
<philippe.m...@gmail.com> wrote:
> Hi,
>
> I am trying to use the Barcode splitter tool as part of a workflow, I am not
> happy with the html output produce by this tool and would like to have
> access to fasta files.
> Any suggestions on how I can modify the tool so that it produces fasta
> outputs that would appear in the workflow ? Thanks
>
> Philippe
>
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<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.

.. image:: ${static_path}/fastx_icons/barcode_splitter_output_example.png

------

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

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

Attachment: fastx_barcode_splitter_single_galaxy_wrapper.py
Description: Binary data

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