comparison ngs-tools_split_by_barcode.xml @ 4:f40640700846 draft

Uploaded

3:5cb5f350b053

    <requirements>
        <requirement type="package" version="0.1.4">ngs-tools</requirement>
    </requirements>
    <command>
        ngs-tools split-by-barcode
            $keep_barcode $input_format.format
            --barcode-size $barcode_length --max-distance $max_distance
            #for $i in $barcodes
              --barcode ${i.barcode}
            #end for
            --report $output1 --galaxy $output1.id --output $__new_file_path__

        <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." />
        <repeat name="barcodes" title="Barcode" help="Barcodes to use. By default all barcodes with the correct length in the index are used. By using this option you can limit which ones to use.">
            <param name="barcode" type="text" label="Barcode to use" />
        </repeat>
        <param name="keep_barcode" type="select" label="Do not trim the barcode" help="By default barcodes are trimmed from the resulting splitted datasets">
            <option value="" selected="true">No</option>
            <option value="--keep-barcode">Yes</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>

4:f40640700846

    <requirements>
        <requirement type="package" version="0.1.4">ngs-tools</requirement>
    </requirements>
    <command>
        ngs-tools split-by-barcode
            $trim_barcode $input_format.format
            --barcode-size $barcode_length --max-distance $max_distance
            #for $i in $barcodes
              --barcode ${i.barcode}
            #end for
            --report $output1 --galaxy $output1.id --output $__new_file_path__

        <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." />
        <repeat name="barcodes" title="Barcode" help="Barcodes to use. By default all barcodes with the correct length in the index are used. By using this option you can limit which ones to use.">
            <param name="barcode" type="text" label="Barcode to use" />
        </repeat>
        <param name="trim_barcode" type="select" label="Trim the barcode" help="By default barcodes are trimmed from the resulting splitted 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>