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<tool id="idba_ud" name="idba_ud" version="1.1.1 (Oct 18, 2012)">
	<description>IDBA-UD - Iterative de Bruijn Graph Assembler for sequencing data with highly uneven depth.</description>
	<command>

	idba_ud

	--read $read

	#if $long_read:

	--long_read $long_read

	#end if

	#if $read_level_2:

		--read_level_2 $read_level_2

	#end if

	#if $read_level_3:

		--read_level_3 $read_level_3

	#end if

	#if $read_level_4:

		--read_level_4 $read_level_4

	#end if

	#if $read_level_5:

		--read_level_5 $read_level_5

	#end if

	--mink $mink --maxk $maxk $step --inner_mink $inner_mink --inner_step $inner_step --prefix $prefix --min_count $min_count --min_support $min_support --num_threads $num_threads --seed_kmer $seed_kmer --min_contig $min_contig --similar $similar --max_mismatch $max_mismatch --min_pairs $min_pairs

	#if str( $other ) != "None":

		$other

	#end if

	;

	mv out/scaffold.fa $output

	</command>

	<inputs>
		<param name="read" type="data" format="fasta" label="Fasta read file. Lower or equal to 250b (--read)"/>
		<param name="long_read" type="data" format="fasta" optional="true" label="Fasta long read file. More than 250b (--long_read)"/>

		<param name="read_level_2" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for second level scaffolds (--read_level_2)"/>
		<param name="read_level_3" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for third level scaffolds (--read_level_3)"/>
		<param name="read_level_4" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for fourth level scaffolds (--read_level_4)"/>
		<param name="read_level_5" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for fifth level scaffolds (--read_level_5)"/>

		<param name="mink" type="integer" value="20" max="124" label="Minimum k value. Lower or equal to 124 (--mink)"/>
		<param name="maxk" type="integer" value="100" max="124" label="Maximum k value. Lower or equal to 124 (--maxk)"/>
		<param name="step" type="integer" value="20" label="Increment of k-mer of each iteration (--step)"/>
		<param name="inner_mink" type="integer" value="10" label="Inner minimum k value (--inner_mink)"/>
		<param name="inner_step" type="integer" value="5" label="Inner increment of k-mer (--inner_step)"/>
		<param name="prefix" type="integer" value="3" label="Prefix length used to build sub k-mer table (--prefix)"/>
		<param name="min_count" type="integer" value="2" label="Minimum multiplicity for filtering k-mer when building the graph (--min_count)"/>
		<param name="min_support" type="integer" value="1" label="Minimum supoort in each iteration (--min_support)"/>
		<param name="num_threads" type="integer" value="0" label="Number of threads (--num_threads)"/>
		<param name="seed_kmer" type="integer" value="30" label="Seed kmer size for alignment (--seed_kmer)"/>
		<param name="min_contig" type="integer" value="200" label="Minimum size of contig (--min_contig)"/>
		<param name="similar" type="float" value="0.95" label="Similarity for alignment (--similar)"/>
		<param name="max_mismatch" type="integer" value="3" label="Max mismatch of error correction (--max_mismatch)"/>
		<param name="min_pairs" type="integer" value="3" label="Minimum number of pairs (--min_pairs)"/>

		<param name="other" type="select" display="checkboxes" separator=" " multiple="true" label="Other options">
			<option value="--no_bubble">Do not merge bubble (--no_bubble)</option>
			<option value="--no_local">Do not use local assembly (--no_local)</option>
			<option value="--no_coverage">Do not iterate on coverage (--no_coverage)</option>
			<option value="--no_correct">Do not do correction (--no_correct)</option>
			<option value="--pre_correction">Perform pre-correction before assembly (--pre_correction)</option>
		</param>
	</inputs>

	<outputs>
		<data name="output" format="fasta"/>
	</outputs>

</tool>