Mercurial > repos > iuc > idba_ud

annotate macros.xml @ 2:694b0f55b744 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 665baeb11498ceef8abb1f1da43fe315d2d75b37"
author iuc
date Tue, 04 Aug 2020 05:50:30 -0400
parents 2ed5c0795f99
children 1542a2fffe0c
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fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
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1 <macros>
1
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2 <token name="@IDBA_VERSION@">1.1.3</token>
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fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
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3 <xml name="requirements">
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
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4 <requirements>
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5 <requirement type="package" version="@IDBA_VERSION@">idba</requirement>
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fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
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6 <yield/>
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
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7 </requirements>
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
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8 </xml>
1
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10 <xml name="main_input">
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11 <param argument="--read" type="data" format="fasta" label="Fasta read file. Lower or equal to 600b"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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12 <param argument="--long_read" type="data" format="fasta" optional="true" label="Fasta long read file. More than 600b"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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13 </xml>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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14
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15 <token name="@MAIN_INPUT@">
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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16 --read '$read'
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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17 #if $long_read:
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18 --long_read '$long_read'
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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19 #end if
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20 </token>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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21
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22 <xml name="levels_input">
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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23 <param argument="--read_level_2" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for second level scaffolds"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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24 <param argument="--read_level_3" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for third level scaffolds"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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25 <param argument="--read_level_4" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for fourth level scaffolds"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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26 <param argument="--read_level_5" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for fifth level scaffolds"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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27 </xml>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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28 <token name="@LEVELS_INPUT@">
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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29 #if $read_level_2:
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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30 --read_level_2 '$read_level_2'
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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31 #end if
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32 #if $read_level_3:
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33 --read_level_3 '$read_level_3'
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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34 #end if
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35 #if $read_level_4:
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36 --read_level_4 '$read_level_4'
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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37 #end if
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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38 #if $read_level_5:
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39 --read_level_5 '$read_level_5'
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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40 #end if
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41 </token>
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42
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43 <xml name="kmer_options" token_maxk_default="" token_step_default="">
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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44 <param argument="--mink" type="integer" value="20" max="312" label="Minimum k value. Lower or equal to 312"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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45 <param argument="--maxk" type="integer" value="@MAXK_DEFAULT@" max="312" label="Maximum k value. Lower or equal to 312"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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46 <param argument="--step" type="integer" value="@STEP_DEFAULT@" label="Increment of k-mer of each iteration"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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47 <param argument="--inner_mink" type="integer" value="10" label="Inner minimum k value"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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48 <param argument="--inner_step" type="integer" value="5" label="Inner increment of k-mer"/>
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49 <param argument="--prefix" type="integer" value="3" label="Prefix length used to build sub k-mer table"/>
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50 <param argument="--min_count" type="integer" value="2" label="Minimum multiplicity for filtering k-mer when building the graph"/>
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51 <param argument="--min_support" type="integer" value="1" label="Minimum supoort in each iteration"/>
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52 <param argument="--seed_kmer" type="integer" value="30" label="Seed kmer size for alignment"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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53 </xml>
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54 <token name="@KMER_OPTIONS@">
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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55 --mink $mink
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56 --maxk $maxk
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57 --step $step
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58 --inner_mink $inner_mink
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59 --inner_step $inner_step
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60 --prefix $prefix
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61 --min_count $min_count
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62 --min_support $min_support
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63 --seed_kmer $seed_kmer
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64 </token>
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65
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66 <xml name="filter_options">
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67 <param argument="--min_contig" type="integer" value="200" label="Minimum size of contig"/>
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68 <param argument="--similar" type="float" value="0.95" label="Similarity for alignment"/>
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69 <param argument="--max_mismatch" type="integer" value="3" label="Max mismatch of error correction"/>
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70 </xml>
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71 <token name="@FILTER_OPTIONS@">
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72 --min_contig $min_contig
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73 --similar $similar
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74 --max_mismatch $max_mismatch
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75 </token>
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76
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77 <xml name="min_pairs_filter">
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78 <param argument="--min_pairs" type="integer" value="3" label="Minimum number of pairs"/>
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79 </xml>
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80 <token name="@MIN_PAIRS_FILTER@">
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81 --min_pairs $min_pairs
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82 </token>
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83 <xml name="other_options">
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84 <param name="other" type="select" display="checkboxes" multiple="true" label="Other options">
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85 <yield/>
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86 <option value="--no_local">Do not use local assembly (--no_local)</option>
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87 <option value="--no_coverage">Do not iterate on coverage (--no_coverage)</option>
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88 <option value="--no_correct">Do not do correction (--no_correct)</option>
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89 <option value="--pre_correction">Perform pre-correction before assembly (--pre_correction)</option>
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90 </param>
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91 </xml>
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92 <token name="@OTHER_OPTIONS@">
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93 #if $other:
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94 ${" ".join(str($other).split(","))}
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95 #end if
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96 </token>
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97
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98 <token name="@THREADS@">
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99 --num_threads \${GALAXY_SLOTS:-1}
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100 </token>
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101
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102 <xml name="help" token_more_help="">
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103 <help><![CDATA[
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104 IDBA is an iterative De Bruijn Graph De Novo Assembler for sequence assembly. Most assemblers based on de Bruijn graph build a de Bruijn graph with a specific k-mer size to perform the assembling task. For all of them, it is very crucial to find a specific value of k. If k is too large, there will be a lot of gap problems in the graph. If k is too small, there will a lot of branch problems. IDBA uses not only one specific k but a range of k values to build the iterative de Bruijn graph. It can keep all the information in graphs with different k values.
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105
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106 @MORE_HELP@
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107
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108 Input: IDBA-* take interleaved paired end data in the FASTA format as input,
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109 i.e. paired-end reads need to be stored in the same FASTA file such that a pair
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110 of reads should be in two consecutive lines.
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111 In Galaxy paired reads in separate FASTQ files can be converted into interleaved
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112 FASTA using the tools:
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113
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114 * `FASTQ interlacer on paired end read <https://toolshed.g2.bx.psu.edu/view/devteam/fastq_paired_end_interlacer>`_
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115 * `Samtools extract FASTA or FASTQ from a SAM file <https://toolshed.g2.bx.psu.edu/view/devteam/fastq_to_fasta>`_
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116
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117 Note that, IDBA-* assumes that the paired-end reads are in order (->,<-).
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118 If your data is in reverse order (<-,->), please convert it by yourself.
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119 ]]></help>
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120 </xml>
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121 <xml name="citations">
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122 <citations>
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123 <citation type="doi">10.1007/978-3-642-12683-3_28</citation>
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124 <yield/>
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125 </citations>
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126 </xml>
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127
0
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128 </macros>