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1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.7" >
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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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2
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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">last</requirement>
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12 <requirement type="package">imagemagick</requirement>
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13 <requirement type="package">mafft</requirement>
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14 <requirement type="package">blast</requirement>
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15 <requirement type="package">diamond</requirement>
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16 <requirement type="package">blast-legacy</requirement>
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17 <requirement type="package">r-igraph</requirement>
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18 <requirement type="package">r-data.tree</requirement>
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19 <requirement type="package">r-stringr</requirement>
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20 <requirement type="package">r-r2html</requirement>
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21 <requirement type="package">r-hwriter</requirement>
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22 <requirement type="package">r-dt</requirement>
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23 <requirement type="package">r-scales</requirement>
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24 <requirement type="package">r-plotrix</requirement>
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25 <requirement type="package">r-png</requirement>
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26 <requirement type="package">r-plyr</requirement>
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27 <requirement type="package">r-dplyr</requirement>
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28 <requirement type="package">r-optparse</requirement>
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29 <requirement type="package">r-dbi</requirement>
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30 <requirement type="package">r-rsqlite</requirement>
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31 <requirement type="package">r-rserve</requirement>
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32 <requirement type="package">bioconductor-biostrings</requirement>
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33 <requirement type="package" version="2.3.7">repex_tarean</requirement>
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34 <requirement type="set_environment">REPEX</requirement>
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35 <requirement type="set_environment">REPEX_VERSION</requirement>
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36 <requirement type="package" version="0.9.1" >pyrserve</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 \${REPEX}/stderr_filter.py stderr.log &&
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64 cd tarean_output &&
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65 zip -r ${ReportArchive}.zip * &&
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66 mv ${ReportArchive}.zip ${ReportArchive} &&
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67 cp index.html ${ReportFile} &&
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68 mkdir ${ReportFile.files_path} &&
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69 cp -r --parents libdir ${ReportFile.files_path} &&
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70 cp -r --parents seqclust/clustering/superclusters ${ReportFile.files_path} &&
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71 cp -r --parents seqclust/clustering/clusters ${ReportFile.files_path} &&
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72 cp seqclust/clustering/hitsort.cls ${ReportFile.files_path}/seqclust/clustering/hitsort.cls &&
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73 cp *.png ${ReportFile.files_path}/ &&
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74 cp *.csv ${ReportFile.files_path}/ &&
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75 cp *.html ${ReportFile.files_path}/ &&
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76 cp *.css ${ReportFile.files_path}/ &&
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77 cp *.fasta ${ReportFile.files_path}/ 2>>$log && rm -r ../tarean_output || :
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78
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79 </command>
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80 <inputs>
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81 <param name="FastaFile" label="NGS reads" type="data" format="fasta"
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82 help="Input file must contain FASTA-formatted NGS reads. Illumina paired-end reads are recommended."/>
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83 <param name="paired" type="boolean" truevalue="--paired" falsevalue="" checked="True" label="Paired-end reads" help="If paired-end reads are used, left- and right-hand reads must be interlaced and all pairs must be complete. Example of the correct format is provided in the help below." />
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84
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85 <param name="sample" label="Sample size" type="integer" value="500000" min="10000"/>
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86 <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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87 <option value="VIRIDIPLANTAE3.0" selected="true">Viridiplantae version 3.0 </option>
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88 <option value="VIRIDIPLANTAE2.2" selected="true">Viridiplantae version 2.2</option>
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89 <option value="METAZOA3.0" >Metazoa version 3.0</option>
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90 <option value="METAZOA2.0" >Metazoa version 2.0</option>
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91 <!-- Modify setting in config.py accordingly -->
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92 </param>
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93
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94 <conditional name="advanced_options">
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95 <param name="advanced" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Advanced options" />
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96 <when value="false">
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97 <!-- pass -->
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98 </when>
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99 <when value="true">
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100 <conditional name="comparative">
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2
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101 <param name="options_comparative" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Perform comparative analysis" help="Use this options to analyze multiple samples simultaneously"/>
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102 <when value="false">
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103 <!-- do nothing here -->
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104 </when>
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105 <when value="true">
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2
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106 <param name="prefix_length" label="Group code length" type="integer" value="3" min="1" max="10" help="For comparative analysis, reads from different samples are distinguished by sample codes included as prefix to the read names. See example below."/>
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107 </when>
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108 </conditional>
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109
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110 <conditional name="blastx">
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111 <param name="options_blastx" type="select" label="Select parameters for protein domain search">
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112 <option value="BLASTX_W2" selected="false">blastx with word size 2 (the most sensitive, slowest)</option>
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113 <option value="BLASTX_W3" selected="true">blastx with word size 3 (default)</option>
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114 <option value="DIAMOND" selected="false">diamond program (the least sensitive, fastest)</option>
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115 </param>
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116 </conditional>
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117
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118 <conditional name="options">
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119 <param name="options" type="select" label="Similarity search options" help="Different similarity search parameters are used depending on the input data to adjust for differences in read length and error rate">
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120 <option value="ILLUMINA" selected="true">Illumina reads, read length 100nt or more </option>
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121 <option value="ILLUMINA_SHORT" selected="false">Illumina reads, shorter than 100nt (Do not use reads shorter than 50nt!) </option>
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122 <option value="ILLUMINA_DUST_OFF" selected="false">Illumina reads, no masking of low complexity repeats </option>
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123 <option value="OXFORD_NANOPORE" selected="false">
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124 Pseudo short reads simulated from Oxford Nanopore data (experimental feature)
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125 </option>
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126 </param>
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127 </conditional>
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128
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129 <conditional name="custom_library">
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130 <param name="options_custom_library" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Use custom repeat database"/>
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131 <when value="false">
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132 <!-- do nothing here -->
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133 </when>
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134 <when value="true">
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2
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135 <param name="library" format="fasta" type="data" label="Custom repeat database" help="The database should contain DNA sequences in FASTA format. The required format for sequence IDs is : '>reapeatname#class/subclass'"/>
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136 </when>
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137 </conditional>
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2
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138 <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; clusters with less than 20 reads are not considered."/>
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139 <param name="automatic_filtering" label="Perform automatic filtering of abundant satellite repeats" help="Automatic filtering identifies the most abundant tandem repeats and partially removes their reads from the analysis. This enables to analyze higher proportions of other less abundant repeats." type="boolean" truevalue="--automatic_filtering" falsevalue="" checked="false"/>
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140 <param name="keep_names" label="Keep original read names" type="boolean" truevalue="--keep_names" falsevalue="" checked="false" help="By default, reads are renamed using integers. Use this option to keep original names."/>
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141 <param name="assembly_min_cluster_size" type="integer" label="Minimal cluster size for assembly" value="5" min="2" max="100"/>
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0
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142 </when>
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143 </conditional>
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144
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145 <conditional name="queue_definition">
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146 <param name="queue_select" type="select" label="Select queue">
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147 <option value="basic_fast_queue">basic (max runtime 2 days, 4 GB RAM)</option>
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148 <option value="long_slow_queue">long (max runtime 2 weeks, 64 GB RAM)</option>
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149 <option value="extra_long_slow_queue">extra long (max runtime 4 weeks, 64 GB RAM)</option>
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150 </param>
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151 <when value="basic_fast_queue">
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152 <param name="queue_specification" type="text" label="Modify parameters (optional)"
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153 value="-l select=1:ncpus=10:mem=32gb:scratch_local=50gb -l walltime=48:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=4000000,TAREAN_CPU=4" />
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154 </when>
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155
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156 <when value="long_slow_queue">
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157 <param name="queue_specification" type="text" label="Modify parameters (optional)"
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158 value="-l select=1:ncpus=16:mem=112gb:scratch_local=50gb -l walltime=336:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=64000000,TAREAN_CPU=15" />
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159 </when>
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160 <when value="extra_long_slow_queue">
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161 <param name="queue_specification" type="text" label="Modify parameters (optional)"
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162 value="-l select=1:ncpus=16:mem=112gb:scratch_local=50gb -l walltime=720:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=64000000,TAREAN_CPU=15" />
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163 </when>
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164 </conditional>
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165
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166
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167
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168 </inputs>
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169 <outputs>
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170 <data name="log" format="txt" label="RepeatExplorer2 - log file"/>
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171 <data name="ReportArchive" format="zip" label="RepeatExplorer2 - Archive with HTML report from data ${FastaFile.hid}"/>
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172 <data name="ReportFile" format="html" label="RepeatExplorer2 - HTML report from data ${FastaFile.hid}"/>
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173 </outputs>
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174
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175 <help>
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176 **HELP**
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177
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178 RepeatExplorer2 clustering is a computational pipeline for unsupervised
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179 identification of repeats from unassembled sequence reads. The
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180 pipeline uses low-pass whole genome sequence reads and performs graph-based
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181 clustering. Resulting clusters, representing all types of repeats, are then
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182 examined to identify and classify into repeats groups.
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183
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184 **Input data**
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185
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186 The analysis requires either **single** or **paired-end reads** generated
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187 by whole genome shotgun sequencing provided as a single fasta-formatted file.
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188 Generally, paired-end reads provide significantly better results than single
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189 reads. Reads should be of uniform length (optimal size range is 100-200 nt) and
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190 the number of analyzed reads should represent less than 1x genome equivalent
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191 (genome coverage of 0.01 - 0.50 x is recommended). Reads should be
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192 quality-filtered (recommended filtering : quality score >=10 over 95% of bases
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193 and no Ns allowed) and only **complete read pairs** should be submitted for
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194 analysis. When paired reads are used, input data must be **interlaced** format
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195 as fasta file:
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196
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197 example of interlaced input format::
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198
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199 >0001_f
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200 CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG
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201 >0001_r
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202 GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT
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203 >0002_f
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204 ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG
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205 >0002_r
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206 TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC
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207 >0003_f
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208 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
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209 >0003_r
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210 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
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211 ...
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212
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213
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214 **Comparative analysis**
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215
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216 For comparative analysis sequence names must contain code (prefix) for each group.
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217 Prefix in sequences names must be of fixed length.
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218
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219 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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220
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221 >AA0001_f
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222 CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG
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223 >AA0001_r
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224 GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT
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225 >AA0002_f
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226 ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG
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227 >AA0002_r
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228 TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC
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229 >BB0001_f
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230 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
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231 >BB0001_r
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232 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
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233 >BB0002_f
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234 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
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235 >BB0002_r
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236 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
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237
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238
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239 To prepare quality filtered and interlaced input fasta file from fastq
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240 files, use `Preprocessing of paired-reads`__ tool.
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241
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242 .. __: tool_runner?tool_id=paired_fastq_filtering
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243
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244
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245 **Additional parameters**
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246
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247 **Sample size** defines how many reads should be used in calculation.
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248 Default setting with 500,000 reads will enable detection of high copy
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249 repeats within several hours of computation time. For higher
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250 sensitivity the sample size can be set higher. Since sample size affects
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251 the memory usage, this parameter may be automatically adjusted to lower
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252 value during the run. Maximum sample size which can be processed depends on
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253 the repetitiveness of analyzed genome.
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254
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255
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256 **Select taxon and protein domain database version (REXdb)**. Classification
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257 of transposable elements is based on the similarity to our reference database
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258 of transposable element protein domains (**REXdb**). Standalone database for Viridiplantae species
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259 can be obtained on `repeatexplorer.org`__. Classification
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260 system used in REXdb is described in article `Systematic survey of plant
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261 LTR-retrotransposons elucidates phylogenetic relationships of their
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262 polyprotein domains and provides a reference for element classification`__
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263 Database for Metazoa species is still under development so use it with caution.
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264
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265 .. __: http://repeatexplorer.org
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266 .. __: https://doi.org/10.1186/s13100-018-0144-1
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267
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268 **Select parameters for protein domain search** REXdb is compared with s
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269 equence clusters either using blastx or diamond aligner. Diamond program
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270 is about three time faster than blastx with word size 3.
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271
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272 **Similarity search options** By default sequence reads are compared using
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273 mgblast program. Default threshold is explicitly set to 90% sequence
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274 similarity spanning at least 55% of the read length (in the case of reads
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275 differing in length it applies to the longer one). Additionally, sequence
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276 overlap must be at least 55 nt. If you select option for shorter reads
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277 than 100 nt, minimum overlap 55 nt is not required.
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278
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279 By default,
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280 mgblast search use DUST program to filter out
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281 low-complexity sequences. If you want
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282 to increase sensitivity of detection of satellites with shorter monomer
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283 use option with '*no masking of low complexity repeats*'. Note that omitting
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284 DUST filtering will significantly increase running times
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285
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286
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287 **Automatic filtering of abundant satellite repeats** perform clustering on
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288 smaller dataset of sequence reads to detect abundant high confidence
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289 satellite repeats. If such satellites are detected, sequence reads derived
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290 from these satellites are depleted from input dataset. This step enable more
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291 sensitive detection of less abundant repeats as more reads can be used
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292 in clustering step.
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293
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294 **Use custom repeat database**. This option allows users to perform similarity
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295 comparison of identified repeats to their custom databases. The repeat class must
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296 be encoded in FASTA headers of database entries in order to allow correct
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297 parsing of similarity hits. Required format for custom database sequence name is: ::
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298
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299 >reapeatname#class/subclass
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300
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301
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302 **Output**
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303
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304 List of clusters identified as putative satellite repeats, their genomic
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305 abundance and various cluster characteristics.
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306
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307 Output includes a **HTML summary** with table listing of all analyzed
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308 clusters. More detailed information about clusters is provided in
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309 additional files and directories. All results are also provided as
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310 downloadable **zip archive**. Additionally a **log file** reporting
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311 the progress of the computational pipeline is provided.
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312
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313 </help>
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314
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315 </tool>
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