Mercurial > repos > stheil > idba_ud_wrapper
comparison idba_ud.xml @ 0:149ae07524e4 draft
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author | stheil |
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date | Thu, 24 Sep 2015 11:58:41 -0400 |
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-1:000000000000 | 0:149ae07524e4 |
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1 <tool id="idba_ud" name="idba_ud" version="1.1.1 (Oct 18, 2012)"> | |
2 <description>IDBA-UD - Iterative de Bruijn Graph Assembler for sequencing data with highly uneven depth.</description> | |
3 <command> | |
4 | |
5 idba_ud | |
6 | |
7 --read $read | |
8 | |
9 #if $long_read: | |
10 | |
11 --long_read $long_read | |
12 | |
13 #end if | |
14 | |
15 #if $read_level_2: | |
16 | |
17 --read_level_2 $read_level_2 | |
18 | |
19 #end if | |
20 | |
21 #if $read_level_3: | |
22 | |
23 --read_level_3 $read_level_3 | |
24 | |
25 #end if | |
26 | |
27 #if $read_level_4: | |
28 | |
29 --read_level_4 $read_level_4 | |
30 | |
31 #end if | |
32 | |
33 #if $read_level_5: | |
34 | |
35 --read_level_5 $read_level_5 | |
36 | |
37 #end if | |
38 | |
39 --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 | |
40 | |
41 #if str( $other ) != "None": | |
42 | |
43 $other | |
44 | |
45 #end if | |
46 | |
47 ; | |
48 | |
49 mv out/scaffold.fa $output | |
50 | |
51 </command> | |
52 | |
53 <inputs> | |
54 <param name="read" type="data" format="fasta" label="Fasta read file. Lower or equal to 250b (--read)"/> | |
55 <param name="long_read" type="data" format="fasta" optional="true" label="Fasta long read file. More than 250b (--long_read)"/> | |
56 | |
57 <param name="read_level_2" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for second level scaffolds (--read_level_2)"/> | |
58 <param name="read_level_3" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for third level scaffolds (--read_level_3)"/> | |
59 <param name="read_level_4" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for fourth level scaffolds (--read_level_4)"/> | |
60 <param name="read_level_5" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for fifth level scaffolds (--read_level_5)"/> | |
61 | |
62 <param name="mink" type="integer" value="20" max="124" label="Minimum k value. Lower or equal to 124 (--mink)"/> | |
63 <param name="maxk" type="integer" value="100" max="124" label="Maximum k value. Lower or equal to 124 (--maxk)"/> | |
64 <param name="step" type="integer" value="20" label="Increment of k-mer of each iteration (--step)"/> | |
65 <param name="inner_mink" type="integer" value="10" label="Inner minimum k value (--inner_mink)"/> | |
66 <param name="inner_step" type="integer" value="5" label="Inner increment of k-mer (--inner_step)"/> | |
67 <param name="prefix" type="integer" value="3" label="Prefix length used to build sub k-mer table (--prefix)"/> | |
68 <param name="min_count" type="integer" value="2" label="Minimum multiplicity for filtering k-mer when building the graph (--min_count)"/> | |
69 <param name="min_support" type="integer" value="1" label="Minimum supoort in each iteration (--min_support)"/> | |
70 <param name="num_threads" type="integer" value="0" label="Number of threads (--num_threads)"/> | |
71 <param name="seed_kmer" type="integer" value="30" label="Seed kmer size for alignment (--seed_kmer)"/> | |
72 <param name="min_contig" type="integer" value="200" label="Minimum size of contig (--min_contig)"/> | |
73 <param name="similar" type="float" value="0.95" label="Similarity for alignment (--similar)"/> | |
74 <param name="max_mismatch" type="integer" value="3" label="Max mismatch of error correction (--max_mismatch)"/> | |
75 <param name="min_pairs" type="integer" value="3" label="Minimum number of pairs (--min_pairs)"/> | |
76 | |
77 <param name="other" type="select" display="checkboxes" separator=" " multiple="true" label="Other options"> | |
78 <option value="--no_bubble">Do not merge bubble (--no_bubble)</option> | |
79 <option value="--no_local">Do not use local assembly (--no_local)</option> | |
80 <option value="--no_coverage">Do not iterate on coverage (--no_coverage)</option> | |
81 <option value="--no_correct">Do not do correction (--no_correct)</option> | |
82 <option value="--pre_correction">Perform pre-correction before assembly (--pre_correction)</option> | |
83 </param> | |
84 </inputs> | |
85 | |
86 <outputs> | |
87 <data name="output" format="fasta"/> | |
88 </outputs> | |
89 | |
90 </tool> |