Mercurial > repos > simon-gladman > velvetoptimiser

annotate velvetoptimiser.xml @ 0:1767f46d815e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit e5ceed1446ce5bb1568ce9caa02a273cf5ee5f09
author iuc
date Mon, 19 Mar 2018 15:07:55 -0400
parents
children 12be7d139d5b
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1767f46d815e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit e5ceed1446ce5bb1568ce9caa02a273cf5ee5f09
iuc
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1 <tool id="velvetoptimiser" name="VelvetOptimiser" version="2.2.5">
1767f46d815e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit e5ceed1446ce5bb1568ce9caa02a273cf5ee5f09
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2 <description>Automatically optimize Velvet assemblies</description>
1767f46d815e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit e5ceed1446ce5bb1568ce9caa02a273cf5ee5f09
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3 <requirements>
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4 <requirement type="package" version="1.2.10">velvet</requirement>
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5 <requirement type="package" version="2.2.5">perl-velvetoptimiser</requirement>
1767f46d815e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit e5ceed1446ce5bb1568ce9caa02a273cf5ee5f09
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6 </requirements>
1767f46d815e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit e5ceed1446ce5bb1568ce9caa02a273cf5ee5f09
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7 <version_command>VelvetOptimiser.pl --version</version_command>
1767f46d815e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit e5ceed1446ce5bb1568ce9caa02a273cf5ee5f09
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8 <command detect_errors="exit_code"><![CDATA[
1767f46d815e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit e5ceed1446ce5bb1568ce9caa02a273cf5ee5f09
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9 export OMP_NUM_THREADS=2 &&
1767f46d815e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit e5ceed1446ce5bb1568ce9caa02a273cf5ee5f09
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10 export OMP_THREAD_LIMIT=2 &&
1767f46d815e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit e5ceed1446ce5bb1568ce9caa02a273cf5ee5f09
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11 VelvetOptimiser.pl
1767f46d815e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit e5ceed1446ce5bb1568ce9caa02a273cf5ee5f09
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12 -t "\${GALAXY_SLOTS:-1}"
1767f46d815e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit e5ceed1446ce5bb1568ce9caa02a273cf5ee5f09
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13 -s $start_kmer
1767f46d815e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit e5ceed1446ce5bb1568ce9caa02a273cf5ee5f09
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14 -e $end_kmer
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15 -d out
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16 -f "
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17 #for $i in $files:
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18 -${i.filetype}
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19
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20 #if str($i.paired_type.paired_type_selector) == "paired":
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21
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22 #if $i.__index__ > 1:
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23 -shortPaired$i.__index__
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24 #else
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25 -shortPaired
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26 #end if
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27
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28 -separate '$i.paired_type.input1' '$i.paired_type.input2'
1767f46d815e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser commit e5ceed1446ce5bb1568ce9caa02a273cf5ee5f09
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29 #end if
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30
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31 #if str($i.paired_type.paired_type_selector) == "single"
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32
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33 #if $i.__index__ > 1
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34 -short$i.__index__
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35 #else
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36 -short
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37 #end if
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38
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39 '$i.paired_type.input1'
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40 #end if
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41
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42 #if str($i.paired_type.paired_type_selector) == "paired_collection"
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43 #if $i.__index__ > 1
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44 -shortPaired$i.__index__
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45 #else
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46 -shortPaired
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47 #end if
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48 -separate '$i.paired_type.input1.forward' '$i.paired_type.input1.reverse'
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49 #end if
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50 #if str($i.paired_type.paired_type_selector) == "paired_iv"
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51 #if $i.__index__ > 1
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52 -shortPaired$i.__index__
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53 #else
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54 -shortPaired
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55 #end if
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56 '$i.paired_type.input1'
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57 #end if
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58 #end for
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59 "
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60
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61 ##if str($advanced.advanced_select) == "advanced"
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62 $advanced.verbose
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63 -k '$advanced.optFuncKmer'
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64 -c '$advanced.optFuncCov'
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65 #if str($advanced.velvetg_opts) != ""
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66 -o '$advanced.velvetg_opts'
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67 #end if
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68 -m $advanced.minCutoff
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69 -z $advanced.maxCutoff
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70 ##end if
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71
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72 ]]></command>
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73 <inputs>
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74 <param name="start_kmer" type="integer" value="31" label="Start k-mer size" help="Odd integer, Lower limit of k-mer size range to search for optimum value" />
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75 <param name="end_kmer" type="integer" value="191" label="End k-mer size" help="Odd integer, Upper limit of k-mer size range to search for optimum value" />
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76 <param name="kmer_step" type="integer" value="2" label="K-mer search step size" help="Even integer, the k-mer value step size when searching the range" />
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77
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78 <repeat name="files" title="Input files" min="1">
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79 <param name="filetype" label="Input file type" type="select" help="Input file type">
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80 <option value="fastq">Fastq</option>
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81 <option value="fasta">Fasta</option>
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82 <option value="bam">Bam</option>
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83 </param>
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84 <conditional name="paired_type">
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85 <param name="paired_type_selector" type="select" label="Single or paired end reads" help="Select between paired and single end data">
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86 <option value="paired">Paired</option>
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87 <option value="single">Single</option>
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88 <option value="paired_collection">Paired Collection</option>
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89 <option value="paired_iv">Paired Interleaved</option>
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90 </param>
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91 <when value="paired">
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92 <param name="input1" type="data" format="fastqsanger,fasta,bam" label="Select first set of reads" help="Specify dataset with forward reads"/>
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93 <param name="input2" type="data" format="fastqsanger,fasta,bam" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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94 </when>
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95 <when value="single">
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96 <param name="input1" type="data" format="fastqsanger,fasta,bam" label="Select the reads" help="Specify dataset with the reads"/>
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97 </when>
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98 <when value="paired_collection">
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99 <param name="input1" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
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100 </when>
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101 <when value="paired_iv">
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102 <param name="input1" type="data" format="fastqsanger,fasta,bam" label="Select set of interleaved reads" help="Specify dataset with interleaved paired reads"/>
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103 </when>
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104 </conditional>
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105 </repeat>
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106
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107 <section name="advanced" title="Advanced Options" expanded="false">
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108 <param name="verbose" type="boolean" checked="false" truevalue="-v" falsevalue="" label="Verbose" help="Include verbose velvet output in log file" />
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109 <param name="optFuncKmer" type="text" value="n50" label="K-mer optimisation function" help="See help below for possibilities!"/>
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110 <param name="optFuncCov" type="text" value="Lbp" label="Coverage cutoff optimisation function" help="See help below for possibilities!"/>
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111 <param name="velvetg_opts" type="text" value="" label="Other velvetg options" help="Add any other required velvetg options from the advanced set"/>
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112 <param name="minCutoff" type="integer" value="0" label="Minimum coverage cutoff" help="The minimum coverage cutoff to consider in the optimisation"/>
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113 <param name="maxCutoff" type="float" value="0.8" label="Maximum coverage cutoff" help="The maximum coverage cutoff to consider expressed as a fraction of the calculated expected coverage."/>
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114 </section>
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115 </inputs>
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116
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117 <outputs>
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118 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="out/contigs.fa"/>
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119 <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Contig Stats" from_work_dir="out/stats.txt"/>
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120 <data format="tabular" name="logfile" label="${tool.name} on ${on_string}: Log file" hidden="true" from_work_dir="*_Logfile.txt"/>
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121 </outputs>
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122
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123 <tests>
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124 <test>
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125 <param name="start_kmer" value="21" />
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126 <param name="end_kmer" value="31" />
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127 <param name="files_0|filetype" value="fasta" />
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128 <param name="files_0|paired_type|paired_type_selector" value="single" />
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129 <param name="files_0|paired_type|input1" value="test_reads.fa" ftype="fasta" />
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130 <output name="contigs" ftype="fasta" file="test-contigs.fa" compare="sim_size"/>
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131 </test>
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132 </tests>
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133
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134 <help><![CDATA[
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135 **Velvet Optimiser Overview**
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136
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137 Velvet_ is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
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138
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139 Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.
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140
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141 Read the Velvet `documentation`__ for details on using the Vevlet Assembler.
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142
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143 .. _Velvet: http://www.ebi.ac.uk/~zerbino/velvet/
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144
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145 .. __: http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf
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146
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147 **VelvetOptimiser**
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148
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149 VelvetOptimiser_ was written by Simon Gladman of CSIRO/Melbourne University.
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150
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151 VelvetOptimiser performs a number of velveth and velvetg steps to try and optimise an assembly based on the metrics provided below.
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152
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153 .. _VelvetOptimiser: http://github.com/Slugger70/VelvetOptimiser
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154
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155 Galaxy tool wrapper for newer versions (2.5.5) of Velvet Optimiser. Written by Simon Gladman of Melbourne University.
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156
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157 **Outputs**
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158
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159
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160 **Contigs**
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161
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162 The *contigs.fa* file.
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163 This fasta file contains the sequences of the contigs longer than 2k, where k is the word-length used in velveth. If you have specified a min contig lgth threshold, then the contigs shorter than that value are omitted.
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164 Note that the length and coverage information provided in the header of each contig should therefore be understood in k-mers and in k-mer coverage (cf. 5.1) respectively.
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165 The N's in the sequence correspond to gaps between scaffolded contigs. The number of N's corresponds to the estimated length of the gap. For reasons of compatibility with the archives, any gap shorter than 10bp is represented by a sequence of 10 N's.
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166
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167 **Stats**
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168
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169 The *stats.txt* file.
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170 This file is a simple tabbed-delimited description of the nodes. The column names are pretty much self-explanatory. Note however that node lengths are given in k-mers. To obtain the length in nucleotides of each node you simply need to add k - 1, where k is the word-length used in velveth.
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171 The in and out columns correspond to the number of arcs on the 5' and 3' ends of the contig respectively.
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172 The coverages in columns short1 cov, short1 Ocov, short2 cov, and short2 Ocov are provided in k-mer coverage (5.1).
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173 Also, the difference between # cov and # Ocov is the way these values are computed. In the first count, slightly divergent sequences are added to the coverage tally. However, in the second, stricter count, only the sequences which map perfectly onto the consensus sequence are taken into account.
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174
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175 **LastGraph**
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176
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177 The *LastGraph* file.
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178 This file describes in its entirety the graph produced by Velvet. This file is hidden by default.
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179
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180 **Logfile**
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181
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182 The Velvet Optimiser's logfile. This file is hidden by default
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183
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184 **STDERR**
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185
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186 The Standard Error output of the Optimiser for error messages etc. This file is hidden by default.
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187
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188 **Advanced options**
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189
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190 Verbose : Include verbose velvet output in log file. Good for debugging when things don't work.
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191
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192 Other Velvetg Options : Extra velvetg options to pass through. eg. -long_mult_cutoff -max_coverage etc (default '') See below for details.
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193
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194 Minimum coverage cutoff : The minimum cov_cutoff to be used. (default '0').
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195
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196 Maximum coverage cutoff : The maximum coverage cutoff to consider as a multiplier of the expected coverage. (default '0.8').
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197
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198 K-mer optimisation function : The optimisation function used for k-mer choice. (default 'n50').
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199
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200 Coverage cutoff optimisation function : The optimisation function used for cov_cutoff optimisation. (default 'Lbp').
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201
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202 Velvet optimiser **assembly optimisation functions** can be built from the following variables.
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203
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204 *LNbp* = The total number of Ns in large contigs
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205
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206 *Lbp* = The total number of base pairs in large contigs
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207
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208 *Lcon* = The number of large contigs
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209
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210 *max* = The length of the longest contig
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211
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212 *n50* = The n50
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213
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214 *ncon* = The total number of contigs
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215
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216 *tbp* = The total number of basepairs in contigs
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217
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218 Examples are:
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219
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220 'Lbp' = Just the total basepairs in contigs longer than 1kb
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221
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222 'n50*Lcon' = The n50 times the number of long contigs.
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223
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224 'n50*Lcon/tbp+log(Lbp)' = The n50 times the number of long contigs divided by the total bases in all contigs plus the log of the number of bases in long contigs (as an example only.)
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225
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226 Defaults are:
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227
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228 *n50* for k-mer length optimisation &
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229
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230 *Lbp* for coverage cutoff
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231
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232 **Hash Length**
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233
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234 The hash length, also known as k-mer length, corresponds to the length, in base pairs, of the words being hashed.
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235
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236 The hash length is the length of the k-mers being entered in the hash table. Firstly, you must observe three technical constraints::
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237 - it must be an odd number, to avoid palindromes. If you put in an even number, Velvet will just decrement it and proceed.
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238 - it must be below or equal to MAXKMERHASH length (cf. 2.3.3, by default 31bp), because it is stored on 64 bits
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239 - it must be strictly inferior to read length, otherwise you simply will not observe any overlaps between reads, for obvious reasons.
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240
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241 Now you still have quite a lot of possibilities. As is often the case, it's a trade-off between specificity and sensitivity. Longer kmers bring you more specificity (i.e. less spurious overlaps) but lowers coverage (cf. below)... so there's a sweet spot to be found with time and experience.
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242 We like to think in terms of "k-mer coverage", i.e. how many times has a k-mer been seen among the reads. The relation between k-mer coverage Ck and standard (nucleotide-wise) coverage C is Ck = C * (L - k + 1)/L where k is your hash length, and L you read length.
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243 Experience shows that this kmer coverage should be above 10 to start getting decent results. If Ck is above 20, you might be "wasting" coverage. Experience also shows that empirical tests with different values for k are not that costly to run! VelvetOptimiser automates these tests for you.
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244
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245
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246 **Velvetg options**
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247
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248 -scaffolding yes|no : scaffolding of contigs used paired end information (default: on)
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249
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250 -max_branch_length integer : maximum length in base pair of bubble (default: 100)
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251
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252 -max_divergence floating-point : maximum divergence rate between two branches in a bubble (default: 0.2)
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253
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254 -max_gap_count integer : maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)
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255
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256 -min_pair_count integer : minimum number of paired end connections to justify the scaffolding of two long contigs (default: 5)
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257
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258 -max_coverage floating point : removal of high coverage nodes AFTER tour bus (default: no removal)
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259
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260 -coverage_mask integer : minimum coverage required for confident regions of contigs (default: 1)
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261
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262 -long_mult_cutoff integer : minimum number of long reads required to merge contigs (default: 2)
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263
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264 -paired_exp_fraction double : remove all the paired end connections which less than the specified fraction of the expected count (default: 0.1)
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265
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266 -conserveLong yes|no : preserve sequences with long reads in them (default no)
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267
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268
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269 **Input Files**
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270
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271 Velvet works mainly with fasta and fastq formats. For paired-end reads, the assumption is that each read is next to its mate
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272 read. In other words, if the reads are indexed from 0, then reads 0 and 1 are paired, 2 and 3, 4 and 5, etc.
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273
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274 Supported file formats are::
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275
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276 fasta
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277 fastq
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278 bam
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279
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280 Read categories are::
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281
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282 short (default)
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283 shortPaired
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284 long (for Sanger, 454 or even reference sequences)
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285 longPaired
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286 reference (for pre-mapped sam or bam files - see Velvet manual for details on how to use this option)
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287
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288
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289 ]]></help>
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290 <citations>
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291 <citation type="bibtex">@UNPUBLISHED{GLADMAN2012,
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292 author = "Gladman Simon",
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293 title = "VelvetOptimiser",
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294 year = "2012",
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295 note = "https://github.com/slugger70/VelvetOptimiser"}
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296 </citation>
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297 <citation type="doi">10.1101/gr.074492.107</citation>
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298 <citation type="doi">10.1371/journal.pone.0008407</citation>
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299 </citations>
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300 </tool>