Mercurial > repos > iuc > idba_ud

annotate idba_ud.xml @ 0:fdaf2375d405 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
author iuc
date Fri, 21 Sep 2018 15:25:56 -0400
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children 2ed5c0795f99
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0
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
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1 <tool id="idba_ud" name="IDBA-UD" version="1.1.3">
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2 <description>
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3 Iterative de Bruijn Graph Assembler <!--for sequencing data with highly uneven depth-->
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <command><![CDATA[
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10
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11 idba_ud
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12
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13 --read '$read'
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14 #if $read_level_2:
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15 --read_level_2 '$read_level_2'
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16 #end if
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17 #if $read_level_3:
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18 --read_level_3 '$read_level_3'
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
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19 #end if
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20 #if $read_level_4:
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21 --read_level_4 '$read_level_4'
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22 #end if
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23 #if $read_level_5:
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24 --read_level_5 '$read_level_5'
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25 #end if
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26 #if $long_read:
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27 --long_read '$long_read'
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28 #end if
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29 --mink $mink
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30 --maxk $maxk
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31 --step $step
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32 --inner_mink $inner_mink
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
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33 --inner_step $inner_step
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
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34 --prefix $prefix
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35 --min_count $min_count
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36 --min_support $min_support
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37 --num_threads \${GALAXY_SLOTS:-1}
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38 --seed_kmer $seed_kmer
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
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39 --min_contig $min_contig
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40 --similar $similar
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41 --max_mismatch $max_mismatch
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42 --min_pairs $min_pairs
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43 #if $other:
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44 ${" ".join(str($other).split(","))}
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45 #end if
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46 ]]></command>
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47
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48 <inputs>
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49 <param argument="--read" type="data" format="fasta" label="Fasta read file. Lower or equal to 600b"/>
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50 <param argument="--long_read" type="data" format="fasta" optional="true" label="Fasta long read file. More than 600b"/>
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51
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52 <param argument="--read_level_2" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for second level scaffolds"/>
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53 <param argument="--read_level_3" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for third level scaffolds"/>
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54 <param argument="--read_level_4" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for fourth level scaffolds"/>
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55 <param argument="--read_level_5" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for fifth level scaffolds"/>
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56
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57 <param argument="--mink" type="integer" value="20" max="312" label="Minimum k value. Lower or equal to 312"/>
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58 <param argument="--maxk" type="integer" value="100" max="312" label="Maximum k value. Lower or equal to 312"/>
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59 <param argument="--step" type="integer" value="20" label="Increment of k-mer of each iteration"/>
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60 <param argument="--inner_mink" type="integer" value="10" label="Inner minimum k value"/>
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61 <param argument="--inner_step" type="integer" value="5" label="Inner increment of k-mer"/>
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62 <param argument="--prefix" type="integer" value="3" label="Prefix length used to build sub k-mer table"/>
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63 <param argument="--min_count" type="integer" value="2" label="Minimum multiplicity for filtering k-mer when building the graph"/>
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64 <param argument="--min_support" type="integer" value="1" label="Minimum supoort in each iteration"/>
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65 <param argument="--seed_kmer" type="integer" value="30" label="Seed kmer size for alignment"/>
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66 <param argument="--min_contig" type="integer" value="200" label="Minimum size of contig"/>
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67 <param argument="--similar" type="float" value="0.95" label="Similarity for alignment"/>
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68 <param argument="--max_mismatch" type="integer" value="3" label="Max mismatch of error correction"/>
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69 <param argument="--min_pairs" type="integer" value="3" label="Minimum number of pairs"/>
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70
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71 <param name="other" type="select" display="checkboxes" multiple="true" label="Other options">
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72 <option value="--no_bubble">Do not merge bubble (--no_bubble)</option>
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73 <option value="--no_local">Do not use local assembly (--no_local)</option>
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74 <option value="--no_coverage">Do not iterate on coverage (--no_coverage)</option>
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75 <option value="--no_correct">Do not do correction (--no_correct)</option>
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76 <option value="--pre_correction">Perform pre-correction before assembly (--pre_correction)</option>
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77 </param>
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78 </inputs>
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79 <outputs>
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80 <data name="output" from_work_dir="out/scaffold.fa" format="fasta"/>
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81 </outputs>
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82 <tests>
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83 <test>
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84 <param name="read" value="merged.fa" ftype="fasta"/>
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85 <output name="output" file="out/scaffold.fa" ftype="fasta"/>
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86 </test>
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87 </tests>
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88 <help><![CDATA[
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89 IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions.
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90
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91
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92 Input: IDBA-UD takes interleaved paired end data in the FASTA format as input,
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93 i.e. paired-end reads need to be stored in the same FASTA file suc h that a pair
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94 of reads should be in two consecutive lines.
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95 In Galaxy paired reads in separate FASTQ files can be converted into interleaved
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96 FASTA using the tools:
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97
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98 * `FASTQ interlacer on paired end read <https://toolshed.g2.bx.psu.edu/view/devteam/fastq_paired_end_interlacer>`_
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99 * `Samtools extract FASTA or FASTQ from a SAM file <https://toolshed.g2.bx.psu.edu/view/devteam/fastq_to_fasta>`_
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100
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101 Note that, IDBA-UD assumes that the paired-end reads are in order (->,<-).
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102 If your data is in reverse order (<-,->), please convert it by yourself.
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103 ]]></help>
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104 <citations>
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105 <citation type="doi">10.1093/bioinformatics/bts174</citation>
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106 </citations>
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107 </tool>