view ngs-tools_split_by_barcode.xml @ 2:ee8699b10e83 draft default tip

Updated to use ngs-tools 0.1.8 with better exception handling and proper writing of error messages to sdterr.

<tool id="ngs-tools_split_by_barcode" name="Barcode Splitter (ngs-tools)" force_history_refresh="True" version="1.0.1">
	<description></description>
    <requirements>
        <requirement type="package" version="0.1.8">ngs-tools</requirement>
    </requirements>
    <command>
        ngs-tools split-by-barcode
            $trim_barcode $input_format.format
            --barcode-size $barcode_length --max-distance $max_distance
            #if $barcodes
              --barcodes $barcodes
            #end if
            --report $output1 --galaxy $output1.id --output $__new_file_path__
            $barcode_index
            #for $i in $input_format.inputs
              ${i.input}
            #end for
    </command>

	<inputs>
        <conditional name="input_format">
            <param name="format" type="select" label="Input format">
                <option value="--fastq" selected="true">Fastq</option>
                <option value="">Fasta</option>
            </param>
            <when value="--fastq">
                <repeat name="inputs" title="Dataset" help="Datasets to split.">
                    <param name="input" type="data" label="Dataset to split" format="fastq,fastqsanger,fastqsolexa,fastqillumina" />
                </repeat>
            </when>
            <when value="">
                <repeat name="inputs" title="Dataset" help="Datasets to split.">
                    <param name="input" type="data" label="Dataset to split" format="fasta" />
                </repeat>
            </when>
        </conditional>
        <param format="tabular" name="barcode_index" type="data" label="Barcodes index" help="See below for description." />
        <param name="barcode_length" type="integer" size="3" value="11" label="Barcode length" help="Please specify the barcode length." />
        <param name="barcodes" type="text" label="Barcodes to use" help="Comma separated list of barcodes to use. By default all barcodes in the 'Barcodes index' are used." />
        <param name="trim_barcode" type="select" label="Trim the barcode" help="By default barcodes are trimmed from the resulting split datasets">
            <option value="" selected="true">Yes</option>
            <option value="--keep-barcode">No</option>
        </param>
        <param name="max_distance" type="integer" size="3" value="2" label="Number of allowed polymorphisms" help="Max Levenshtein's distance when looking for mutated barcodes." />
	</inputs>
	
	<outputs>
		<data format="tabular" name="output1" />
	</outputs>
    <help>

**What it does**

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

--------

**Barcode index format**

Barcode index datasets are simple tab separated 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::

    RL001   ACACGACGACT
    RL002   ACACGTAGTAT
    RL003   ACACTACTCGT
    RL004   ACGACACGTAT
    RL005   ACGAGTAGACT
    
For each barcode, a new FASTQ or FASTA dataset will be created (with the barcode's identifier as part of the dataset name).
Sequences matching the barcode will be stored in the appropriate dataset.

One additional FASTQ or FASTA dataset will be created (the 'Unassigned' dataset), where sequences not matching any barcode will be stored.

The output of this tool is one history dataset per each barcode provided plus a report with the split counts.

------

This tool is based on `ngs-tools`__ by Carlos Borroto &lt;[e-mail]&gt;.

 .. __: https://github.com/cjav/ngs-tools/
 
    </help>
</tool>