comparison ngs-tools_split_by_barcode.xml @ 2:5a9ba0f9ea6f draft

Uploaded

1:25b250eeccda

<tool id="ngs-tools_split_by_barcode" name="Barcode Splitter (ngs-tools)" force_history_refresh="True">
	<description></description>
	<requirements><requirement type="package">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

              ${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." />
        <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">

2:5a9ba0f9ea6f

<tool id="ngs-tools_split_by_barcode" name="Barcode Splitter (ngs-tools)" force_history_refresh="True">
	<description></description>
    <command>
        ngs-tools split-by-barcode
            $keep_barcode $input_format.format
            --barcode-size $barcode_length --max-distance $max_distance
            #for $i in $barcodes

              ${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." />
        <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">