comparison umi-tools_whitelist.xml @ 16:953b4821b183 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit 31bad8c5bf75981eafcd19ec6b00593f184fdeb8"

15:81bebc3027fc

        <expand macro="input_types" />
        <expand macro="fastq_barcode_extraction_options_macro"/>

        <param argument="--method" type="select" label="Count reads or UMIs"
               help="Many published protocols rank CBs by the number of reads the CBs appear in. However you could also use the number of unique UMIs a CB is associated with. Note that this is still and approximation to the number of transcripts captured because the same UMI could be associated with two different transcripts and be counted as independent" >
            <option value="reads" selected="true" />
            <option value="umis" />
        </param>
        <!-- TODO Cannot use expect-cells with 'distance' knee method.-->
        <param argument="--knee-method" type="select" label="Method for detection of knee">
            <option value="distance" selected="true" />
            <option value="density"/>
        </param>
        <param argument="--subset-reads" type="integer" min="0" value="0" label="Use the first N reads to automatically identify the true cell barcodes" />
        <param argument="--allow-threshold-error" type="boolean" truevalue="--allow-threshold-error" falsevalue="" label="Don't select a threshold" help="Will still output the plots if requested"/> 
        <param argument="--ed-above-threshold" type="select" optional="true" label="Detect and correct CBs above the threshold" help="which may be sequence errors from another CB">
            <option value="correct">correct</option>
            <option value="discard">discard</option>
        </param>
        <conditional name="celloptions" >
            <param name="use_cell_opts" type="select" label="Cell parameters" >
                <option value="defaults" selected="True">Use Defaults</option>
                <option value="advanced">Advanced Options</option>

16:953b4821b183

        <expand macro="input_types" />
        <expand macro="fastq_barcode_extraction_options_macro"/>

        <param argument="--method" type="select" label="Count reads or UMIs"
               help="Many published protocols rank CBs by the number of reads the CBs appear in. However you could also use the number of unique UMIs a CB is associated with. Note that this is still and approximation to the number of transcripts captured because the same UMI could be associated with two different transcripts and be counted as independent" >
            <option value="reads" selected="true">Reads</option>
            <option value="umis">UMIs</option>
        </param>
        <!-- TODO Cannot use expect-cells with 'distance' knee method.-->
        <param argument="--knee-method" type="select" label="Method for detection of knee">
            <option value="distance" selected="true">Distance</option>
            <option value="density">Density</option>
        </param>
        <param argument="--subset-reads" type="integer" min="0" value="0" label="Use the first N reads to automatically identify the true cell barcodes" />
        <param argument="--allow-threshold-error" type="boolean" truevalue="--allow-threshold-error" falsevalue="" label="Don't select a threshold" help="Will still output the plots if requested"/> 
        <param argument="--ed-above-threshold" type="select" optional="true" label="Detect and correct CBs above the threshold" help="which may be sequence errors from another CB">
            <option value="correct">Correct</option>
            <option value="discard">Discard</option>
        </param>
        <conditional name="celloptions" >
            <param name="use_cell_opts" type="select" label="Cell parameters" >
                <option value="defaults" selected="True">Use Defaults</option>
                <option value="advanced">Advanced Options</option>