changeset 0:149ae07524e4 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/idba_ud.xml	Thu Sep 24 11:58:41 2015 -0400
@@ -0,0 +1,90 @@
+<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>