comparison create_ribosome_profile/create_ribosome_profile.xml @ 6:8f8affaa5eb4 draft

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5:4d69f7428243

            #else:
                ${refGenomeSource.input1_file} none ${input4} ${output1}
            #end if
    </command>
    <inputs>
        <conditional name="refGenomeSource">
            <param name="input1" type="data" format="bam" label="BAM file to process"/>
            <param name="input2" type="integer" value="15" label="Offset to use" help="Use 15 for elongating ribosomes, 12 for initiating and 0 form RNA-seq reads"/>
            <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in FASTA?">
                <option value="builtin">Use a built-in FASTA</option>
                <option value="history">Use one from the history</option>
            </param>
            <when value="builtin">

6:8f8affaa5eb4

            #else:
                ${refGenomeSource.input1_file} none ${input4} ${output1}
            #end if
    </command>
    <inputs>
        <param name="input1" type="data" format="bam" label="BAM file to process"/>
        <param name="input2" type="integer" value="15" label="Offset to use" help="Use 15 for elongating ribosomes, 12 for initiating and 0 form RNA-seq reads"/>
        <conditional name="refGenomeSource">
            <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in FASTA?">
                <option value="builtin">Use a built-in FASTA</option>
                <option value="history">Use one from the history</option>
            </param>
            <when value="builtin">