view macros.xml @ 10:d00e18a0a3f2

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<macros>
	<xml name="requirements">
		<requirements>
			<!-- <requirement type="binary">@BINARY@</requirement> -->
			<requirement type="package" version="1.1">khmer</requirement>
		</requirements>
		<version_command>@BINARY@ --version</version_command>
	</xml>
	<token name="TABLEPARAMS">#if $parameters.type == "simple"
--ksize=20
--n_tables=4
--min-tablesize=$parameters.tablesize
#else
--ksize=$parameters.ksize
--n_tables=$parameters.n_tables
--min-tablesize=$parameters.tablesize_specific
#end if</token>
	<xml name="tableinputs">
		<conditional name="parameters">
			<param	name="type"
				type="select"
				label="Advanced Parameters"
				help="ksize, n_hashess, a specific hashsize" >
				<option	value="simple"
					selected="true">
					Hide
				</option>
				<option value="specific">
					Show
				</option>
            		</param>
			<when	value="simple">
				<param	name="hashsize"
					type="select"
					label="Sample Type"
					display="radio">
					<option	value="1e9"
						selected="true">
						Microbial Genome
					</option>
					<option value="2e9">
						Animal Transcriptome
					</option>
					<option value="4e9">
						Small Animal Genome or Low-Diversity Metagenome
					</option>
					<option value="16e9">
						Large Animal Genome
					</option>
				</param>
			</when>
			<when	value="specific">
				<param	name="ksize"
					type="integer"
					value="20"
					label="ksize"
					help="k-mer size to use" />
				<param	name="n_hashes"
					type="integer"
					min="1"
					value="4"
					label="n_hashes"
					help="number of hash tables to use" />
				<param	name="hashsize_specifc"
					type="text"
					label="hashsize"
					help="lower bound on the hashsize to use" />
			</when>
		</conditional>
	</xml>
	<xml name="input_sequence_filename">
                <param  name="input_sequence_filename"
                        type="data"
                        format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina"
                        label="FAST[AQ] file(s)" />
	</xml>
	<xml name="input_counting_table_filename">
                <param  name="input_counting_table_filename"
                        type="data"
                        label="the k-mer counting table to query"
                        help="The abundances of the k-mers in the input nucleotide sequence file will be calculated using the kmer counts in this k-mer counting table." />
	</xml>
	<xml name="abundance-histogram-output">
                <data   name="output_histogram_filename"
                        format="text"
                        label="${tool.name} k-mer abundance histogram. The
                        columns are: (1) k-mer abundance, (2) k-mer count, (3)
                        cumulative count, (4) fraction of total distinct
                        k-mers.">
                </data>
	</xml>
</macros>