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1 <tool id="repeatexplorer2x" name="RepeatExplorer2 clustering: " version="2.3.6" >
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0
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2 <stdio>
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3 <regex match="lastdb: can't open file: NEAR" source="stderr" level="fatal" description="Version of last is too old, use ver 956 or higher\n" />
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4 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
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5 <regex match="error" source="stderr" level="fatal" description="Unknown error" />
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6 <regex match="Warning" source="stderr" level="warning" description="Unknown error" />
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7 <exit_code range="1:" level="fatal" description="Error" />
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8 </stdio>
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9 <description>Improved version or repeat discovery and characterization using graph based sequence clustering</description>
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10 <requirements>
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11 <requirement type="package" version="3.7">python</requirement>
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12 <requirement type="package" version="0.9.1" >pyrserve</requirement>
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13 <requirement type="package">last</requirement>
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0
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14 <requirement type="package">mafft</requirement>
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15 <requirement type="package">imagemagick</requirement>
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16 <requirement type="package">blast</requirement>
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17 <requirement type="package">diamond</requirement>
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18 <requirement type="package">blast-legacy</requirement>
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19 <requirement type="package">r-igraph</requirement>
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20 <requirement type="package">r-data.tree</requirement>
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21 <requirement type="package">r-stringr</requirement>
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22 <requirement type="package">r-r2html</requirement>
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23 <requirement type="package">r-hwriter</requirement>
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24 <requirement type="package">r-dt</requirement>
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25 <requirement type="package">r-scales</requirement>
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26 <requirement type="package">r-plotrix</requirement>
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27 <requirement type="package">r-png</requirement>
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28 <requirement type="package">r-plyr</requirement>
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29 <requirement type="package">r-dplyr</requirement>
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30 <requirement type="package">r-optparse</requirement>
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31 <requirement type="package">r-dbi</requirement>
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32 <requirement type="package">r-rsqlite</requirement>
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33 <requirement type="package">r-rserve</requirement>
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34 <requirement type="package">bioconductor-biostrings</requirement>
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35 <requirement type="package" version="1.0">repex_tarean</requirement>
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36 <requirement type="set_environment">REPEX</requirement>
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37 </requirements>
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38 <command >
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39 export PYTHONHASHSEED=0;
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40 \${REPEX}/seqclust --sample ${sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon
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41
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42 #if $advanced_options.advanced:
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43 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -D $advanced_options.blastx.options_blastx
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44 --assembly_min $advanced_options.assembly_min_cluster_size
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45
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46 #if $advanced_options.comparative.options_comparative:
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47 --prefix_length $advanced_options.comparative.prefix_length
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48 #end if
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49
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50 #if $advanced_options.custom_library.options_custom_library:
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51 -d $advanced_options.custom_library.library extra_database
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52 #end if
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53
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54 #if $advanced_options.options.options:
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55 -opt $advanced_options.options.options
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56 #end if
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57 #end if
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58 ${FastaFile} >stdout.log 2> stderr.log ;
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59 echo "STDOUT CONTENT:" >> ${log} ;
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60 cat stdout.log >> ${log} ;
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61 echo "STDERR CONTENT:" >> ${log};
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62 cat stderr.log >> ${log} &&
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63 cd tarean_output &&
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64 zip -r ${ReportArchive}.zip * &&
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65 mv ${ReportArchive}.zip ${ReportArchive} &&
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66 cp index.html ${ReportFile} &&
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67 mkdir ${ReportFile.files_path} &&
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68 cp -r --parents libdir ${ReportFile.files_path} &&
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69 cp -r --parents seqclust/clustering/superclusters ${ReportFile.files_path} &&
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70 cp -r --parents seqclust/clustering/clusters ${ReportFile.files_path} &&
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71 cp seqclust/clustering/hitsort.cls ${ReportFile.files_path}/seqclust/clustering/hitsort.cls &&
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72 cp *.png ${ReportFile.files_path}/ &&
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73 cp *.csv ${ReportFile.files_path}/ &&
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74 cp *.html ${ReportFile.files_path}/ &&
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75 cp *.css ${ReportFile.files_path}/ &&
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76 cp *.fasta ${ReportFile.files_path}/ 2>>$log && rm -r ../tarean_output || :
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77
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78 </command>
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79 <inputs>
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80 <param name="FastaFile" label="NGS reads" type="data" format="fasta"
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81 help="Input file must contain fasta-formatted NGS reads. If paired end reads are used, reads must be interlaced and all pairs must be complete. Example of input data format is provided in the help below. "/>
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82 <param name="paired" type="boolean" truevalue="--paired" falsevalue="" checked="True" label="Paired-end reads" help="Check if you are using pair reads and input sequences contain both read mates and left mates alternate with their right mates" />
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83
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84 <param name="sample" label="Sample size" type="integer" value="500000" min="10000"/>
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85 <param name="taxon" label="Select taxon and protein domain database version (REXdb)" type="select" help="Reference database of transposable element protein domains - REXdb - is used for annotation of repeats">
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86 <option value="VIRIDIPLANTAE3.0" selected="true">Viridiplantae version 3.0 </option>
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87 <option value="VIRIDIPLANTAE2.2" selected="true">Viridiplantae version 2.2</option>
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88 <option value="METAZOA3.0" >Metazoa version 3.0</option>
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89 <option value="METAZOA2.0" >Metazoa version 2.0</option>
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90 <!-- Modify setting in config.py accordingly -->
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91 </param>
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92
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93 <conditional name="advanced_options">
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94 <param name="advanced" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Advanced options" />
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95 <when value="false">
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96 <!-- pass -->
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97 </when>
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98 <when value="true">
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99 <conditional name="comparative">
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100 <param name="options_comparative" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Perform comparative analysis" help="Use this options when you want to compare sequences multiple groups"/>
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101 <when value="false">
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102 <!-- do nothing here -->
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103 </when>
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104 <when value="true">
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105 <param name="prefix_length" label="Group code length" type="integer" value="3" min="1" max="10" help="For comparative analysis, sequences are from individial groups distinguished by sample code which must be used as prefix for sequence name. See example below."/>
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106 </when>
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107 </conditional>
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108
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109 <conditional name="blastx">
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110 <param name="options_blastx" type="select" label="Select parameters for protein domain search">
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111 <option value="BLASTX_W2" selected="false">blastx with word size 2 (the most sensitive, slowest)</option>
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112 <option value="BLASTX_W3" selected="true">blastx with word size 3 (default)</option>
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113 <option value="DIAMOND" selected="false">diamond program (the least sensitive, fastest)</option>
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114 </param>
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115 </conditional>
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116
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117 <conditional name="options">
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118 <param name="options" type="select" label="Similarity search options" help="Different similarity search parameters are used depending on the used input data to adjust search to differences in length and error rate">
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119 <option value="ILLUMINA" selected="true">Illumina reads, read length 100nt or more </option>
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120 <option value="ILLUMINA_SHORT" selected="false">Illumina reads, shorter than 100nt (Do not use reads shorter than 50nt!) </option>
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121 <option value="ILLUMINA_DUST_OFF" selected="false">Illumina reads, no masking of low complexity repeats </option>
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122 <option value="OXFORD_NANOPORE" selected="false">
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123 Pseudo short reads simulated from Oxford Nanopore data (experimental feature)
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124 </option>
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125 </param>
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126 </conditional>
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127
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128 <conditional name="custom_library">
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129 <param name="options_custom_library" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Use custom repeat database"/>
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130 <when value="false">
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131 <!-- do nothing here -->
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132 </when>
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133 <when value="true">
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134 <param name="library" format="fasta" type="data" label="Custom library of repeats" help="Library of repeats as DNA sequences in fasta format. The required format for IDs in a custom library is : '>reapeatname#class/subclass'"/>
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135 </when>
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136 </conditional>
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137 <param name="size_threshold" label="Cluster size threshold for detailed analysis" type="float" value="0.01" min="0.0001" max="100" help ="Minimal size (as percentage of input reads) of the smallest cluster which is analyzed, cluster with less than 20 reads are not considered at all."/>
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138 <param name="automatic_filtering" label="Perform automatic filtering of abundant satellite repeats" help="Automatic filtering tries to identify the most abundant tandem repeats and remove such sequences partially from analysis. Removal of abundant tandem repeat can enable to analyze higher proportion of other less abundant repeats." type="boolean" truevalue="--automatic_filtering" falsevalue="" checked="false"/>
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139 <param name="keep_names" label="Keep original sequences names" type="boolean" truevalue="--keep_names" falsevalue="" checked="false" help="By default sequence are relabeled using integers. If you want to keep original names, use this option."/>
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140 <param name="assembly_min_cluster_size" type="integer" label="min cluster size for assembly" value="5" min="2" max="100"/>
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141 </when>
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142 </conditional>
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143
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144 </inputs>
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145 <outputs>
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146 <data name="log" format="txt" label="RepeatExplorer2 - log file"/>
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147 <data name="ReportArchive" format="zip" label="RepeatExplorer2 - Archive with HTML report from data ${FastaFile.hid}"/>
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148 <data name="ReportFile" format="html" label="RepeatExplorer2 - HTML report from data ${FastaFile.hid}"/>
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149 </outputs>
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150
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151 <help>
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152 **HELP**
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153
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154 RepeatExplorer2 clustering is a computational pipeline for unsupervised
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155 identification of repeats from unassembled sequence reads. The
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156 pipeline uses low-pass whole genome sequence reads and performs graph-based
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157 clustering. Resulting clusters, representing all types of repeats, are then
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158 examined to identify and classify into repeats groups.
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159
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160 **Input data**
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161
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162 The analysis requires either **single** or **paired-end reads** generated
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163 by whole genome shotgun sequencing provided as a single fasta-formatted file.
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164 Generally, paired-end reads provide significantly better results than single
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165 reads. Reads should be of uniform length (optimal size range is 100-200 nt) and
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166 the number of analyzed reads should represent less than 1x genome equivalent
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167 (genome coverage of 0.01 - 0.50 x is recommended). Reads should be
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168 quality-filtered (recommended filtering : quality score >=10 over 95% of bases
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169 and no Ns allowed) and only **complete read pairs** should be submitted for
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170 analysis. When paired reads are used, input data must be **interlaced** format
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171 as fasta file:
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172
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173 example of interlaced input format::
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174
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175 >0001_f
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176 CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG
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177 >0001_r
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178 GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT
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179 >0002_f
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180 ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG
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181 >0002_r
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182 TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC
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183 >0003_f
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184 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
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185 >0003_r
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186 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
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187 ...
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188
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189
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190 **Comparative analysis**
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191
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192 For comparative analysis sequence names must contain code (prefix) for each group.
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193 Prefix in sequences names must be of fixed length.
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194
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195 Example of labeling two groups with where **group code length** is 2 and is used to distinguish groups - AA and BB ::
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196
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197 >AA0001_f
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198 CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG
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199 >AA0001_r
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200 GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT
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201 >AA0002_f
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202 ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG
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203 >AA0002_r
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204 TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC
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205 >BB0001_f
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206 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
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207 >BB0001_r
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208 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
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209 >BB0002_f
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210 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
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211 >BB0002_r
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212 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
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213
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214
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215 To prepare quality filtered and interlaced input fasta file from fastq
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216 files, use `Preprocessing of paired-reads`__ tool.
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217
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218 .. __: tool_runner?tool_id=paired_fastq_filtering
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219
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220
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221 **Additional parameters**
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222
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223 **Sample size** defines how many reads should be used in calculation.
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224 Default setting with 500,000 reads will enable detection of high copy
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225 repeats within several hours of computation time. For higher
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226 sensitivity the sample size can be set higher. Since sample size affects
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227 the memory usage, this parameter may be automatically adjusted to lower
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228 value during the run. Maximum sample size which can be processed depends on
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229 the repetitiveness of analyzed genome.
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230
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231
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232 **Select taxon and protein domain database version (REXdb)**. Classification
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233 of transposable elements is based on the similarity to our reference database
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234 of transposable element protein domains (**REXdb**). Standalone database for Viridiplantae species
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235 can be obtained on `repeatexplorer.org`__. Classification
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236 system used in REXdb is described in article `Systematic survey of plant
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237 LTR-retrotransposons elucidates phylogenetic relationships of their
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238 polyprotein domains and provides a reference for element classification`__
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239 Database for Metazoa species is still under development so use it with caution.
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240
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241 .. __: http://repeatexplorer.org
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242 .. __: https://doi.org/10.1186/s13100-018-0144-1
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243
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244 **Select parameters for protein domain search** REXdb is compared with s
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245 equence clusters either using blastx or diamond aligner. Diamond program
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246 is about three time faster than blastx with word size 3.
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247
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248 **Similarity search options** By default sequence reads are compared using
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249 mgblast program. Default threshold is explicitly set to 90% sequence
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250 similarity spanning at least 55% of the read length (in the case of reads
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251 differing in length it applies to the longer one). Additionally, sequence
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252 overlap must be at least 55 nt. If you select option for shorter reads
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253 than 100 nt, minimum overlap 55 nt is not required.
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254
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255 By default,
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256 mgblast search use DUST program to filter out
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257 low-complexity sequences. If you want
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258 to increase sensitivity of detection of satellites with shorter monomer
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259 use option with '*no masking of low complexity repeats*'. Note that omitting
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260 DUST filtering will significantly increase running times
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261
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262
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263 **Automatic filtering of abundant satellite repeats** perform clustering on
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264 smaller dataset of sequence reads to detect abundant high confidence
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265 satellite repeats. If such satellites are detected, sequence reads derived
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266 from these satellites are depleted from input dataset. This step enable more
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267 sensitive detection of less abundant repeats as more reads can be used
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268 in clustering step.
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269
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270 **Use custom repeat database**. This option allows users to perform similarity
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271 comparison of identified repeats to their custom databases. The repeat class must
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272 be encoded in FASTA headers of database entries in order to allow correct
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273 parsing of similarity hits. Required format for custom database sequence name is: ::
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274
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275 >reapeatname#class/subclass
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276
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277
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278 **Output**
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279
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280 List of clusters identified as putative satellite repeats, their genomic
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281 abundance and various cluster characteristics.
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282
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283 Output includes a **HTML summary** with table listing of all analyzed
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284 clusters. More detailed information about clusters is provided in
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285 additional files and directories. All results are also provided as
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286 downloadable **zip archive**. Additionally a **log file** reporting
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287 the progress of the computational pipeline is provided.
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288
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289 </help>
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290
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291 </tool>
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