I just saw the opposite problem which planemo lint could also spot: <when/> blocks which did not match the select, e.g. something like this:

        <conditional name="input_type_conditional">
            <param name="input_type" type="select" label="Input Type">
                <option value="single" selected="true">Single Dataset</option>
                <option value="paired_collection">Paired Collection</option>
                <!-- note missing paired_files here -->
            </param>
            <when value="single">
                 <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with single reads"/>
            </when>
            <when value="paired_files">
                 <param name="fastq_input_f" type="data" format="fastqsanger" label="Select forward fastq dataset" help="Specify dataset with forward reads"/>
                 <param name="fastq_input_r" type="data" format="fastqsanger" label="Select reverse fastq dataset" help="Specify dataset with reverse reads"/>
            </when>
            <when value="paired_collection">
                 <param name="fastq_input" type="data_collection" format="fastqsanger" label="Select dataset pair" help="Specify paired dataset collection containing paired reads" />
            </when>
        </conditional>

Check for missing <when/> blocks #194

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