| Next changeset 1:14f74ce39bb1 (2015-09-24) |
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Commit message:
Uploaded |
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added:
idba_ud.xml |
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| diff -r 000000000000 -r 149ae07524e4 idba_ud.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/idba_ud.xml Thu Sep 24 11:58:41 2015 -0400 |
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| @@ -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> |