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14
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1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.8.2" >
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2
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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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6
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11 <container type="singularity">library://repeatexplorer/default/repex_tarean:0.3.8-dbaa07f</container>
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2
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12 </requirements>
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4
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13 <command>
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2
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14 export PYTHONHASHSEED=0;
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14
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15 export TAREAN_CPU=\$GALAXY_SLOTS;
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16 export TAREAN_MAX_MEM=\$GALAXY_MEMORY_MB;
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4
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17 seqclust --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon
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2
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18
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19 #if $advanced_options.advanced:
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20 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -D $advanced_options.blastx.options_blastx
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21 --assembly_min $advanced_options.assembly_min_cluster_size
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22
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23 #if $advanced_options.comparative.options_comparative:
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24 --prefix_length $advanced_options.comparative.prefix_length
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25 #end if
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26
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27 #if $advanced_options.custom_library.options_custom_library:
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28 -d $advanced_options.custom_library.library extra_database
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29 #end if
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30
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31 #if $advanced_options.options.options:
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32 -opt $advanced_options.options.options
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33 #end if
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34 #end if
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35 ${FastaFile} >stdout.log 2> stderr.log ;
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36 echo "STDOUT CONTENT:" >> ${log} ;
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37 cat stdout.log >> ${log} ;
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38 echo "STDERR CONTENT:" >> ${log};
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39 cat stderr.log >> ${log} &&
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4
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40 /opt/repex_tarean/stderr_filter.py stderr.log &&
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2
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41 cd tarean_output &&
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42 zip -r ${ReportArchive}.zip * &&
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43 mv ${ReportArchive}.zip ${ReportArchive} &&
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2
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44 cp index.html ${ReportFile} &&
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45 mkdir -p ${ReportFile.extra_files_path} &&
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46 cp -r --parents libdir ${ReportFile.extra_files_path} &&
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47 cp -r --parents seqclust/clustering/superclusters ${ReportFile.extra_files_path} &&
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48 cp -r --parents seqclust/clustering/clusters ${ReportFile.extra_files_path} &&
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49 cp seqclust/clustering/hitsort.cls ${ReportFile.extra_files_path}/seqclust/clustering/hitsort.cls &&
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50 cp *.png ${ReportFile.extra_files_path}/ &&
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51 cp *.csv ${ReportFile.extra_files_path}/ &&
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52 cp *.html ${ReportFile.extra_files_path}/ &&
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53 cp *.css ${ReportFile.extra_files_path}/ &&
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54 cp *.fasta ${ReportFile.extra_files_path}/ 2>>$log && rm -r ../tarean_output || :
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2
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55
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56 </command>
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57 <inputs>
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58 <param name="FastaFile" label="NGS reads" type="data" format="fasta"
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59 help="Input file must contain FASTA-formatted NGS reads. Illumina paired-end reads are recommended."/>
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60 <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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61
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62 <conditional name="read_sampling">
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63 <param name="do_sampling" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Read sampling" help="Use this option if you want to analyze only a part of the reads" />
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64 <when value="false">
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65 <!-- pass -->
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66 <param name="sample" label="Sample size" hidden="True" type="integer" value="0" help="Number of analyzed reads"/>
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67 </when>
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68 <when value="true">
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69 <param name="sample" label="Sample size" type="integer" value="500000" min="10000" help="Number of analyzed reads"/>
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70 </when>
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71 </conditional>
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72
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73
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74 <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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75 <option value="VIRIDIPLANTAE3.0" selected="true">Viridiplantae version 3.0 </option>
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76 <option value="VIRIDIPLANTAE2.2" selected="true">Viridiplantae version 2.2</option>
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77 <option value="METAZOA3.0" >Metazoa version 3.0</option>
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78 <option value="METAZOA2.0" >Metazoa version 2.0</option>
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79 <!-- Modify setting in config.py accordingly -->
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80 </param>
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81
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82 <conditional name="advanced_options">
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83 <param name="advanced" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Advanced options" />
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84 <when value="false">
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85 <!-- pass -->
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86 </when>
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87 <when value="true">
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88 <conditional name="comparative">
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89 <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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90 <when value="false">
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91 <!-- do nothing here -->
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92 </when>
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93 <when value="true">
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94 <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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95 </when>
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96 </conditional>
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97
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98 <conditional name="blastx">
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99 <param name="options_blastx" type="select" label="Select parameters for protein domain search">
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100 <option value="BLASTX_W2" selected="false">blastx with word size 2 (the most sensitive, slowest)</option>
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101 <option value="BLASTX_W3" selected="true">blastx with word size 3 (default)</option>
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102 <option value="DIAMOND" selected="false">diamond program (the least sensitive, fastest)</option>
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103 </param>
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104 </conditional>
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105
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106 <conditional name="options">
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107 <param name="options" type="select" label="Similarity search options">
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108 <option value="ILLUMINA" selected="true">Default </option>
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109 <option value="ILLUMINA_DUST_OFF" selected="false">Masking of low complexity repeats disabled </option>
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110
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111 <!-- <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">Illumina reads, sensitive search (search parameters: mgblast, min PID 80, -W8) slow, experimental feature!</option> -->
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112 <!-- <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">Illumina reads, more sensitive search (search parameters: blastn, min PID 80, -W6) extremely slow, experimental feature!</option> -->
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113 <!-- <option value="OXFORD_NANOPORE" selected="false"> -->
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114 <!-- Pseudo short reads simulated from Oxford Nanopore data, experimental feature! -->
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115 <!-- </option> -->
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116 </param>
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117 </conditional>
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118
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119 <conditional name="custom_library">
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120 <param name="options_custom_library" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Use custom repeat database"/>
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121 <when value="false">
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122 <!-- do nothing here -->
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123 </when>
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124 <when value="true">
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125 <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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126 </when>
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127 </conditional>
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128 <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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129 <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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130 <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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131 <param name="assembly_min_cluster_size" type="integer" label="Minimal cluster size for assembly" value="5" min="2" max="100"/>
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132 </when>
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133 </conditional>
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14
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134 <param name="queue_select" type="select" label="Select queue">
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135 <option value="basic_fast_queue">basic (max runtime 2 days, 4 GB RAM)</option>
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136 <option value="long_slow_queue">long (max runtime 2 weeks, 64 GB RAM)</option>
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137 <option value="extra_long_slow_queue">extra long (max runtime 4 weeks, 64 GB RAM)</option>
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138 </param>
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2
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139
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140 </inputs>
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141 <outputs>
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142 <data name="log" format="txt" label="RepeatExplorer2 - log file"/>
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143 <data name="ReportArchive" format="zip" label="RepeatExplorer2 - Archive with HTML report from data ${FastaFile.hid}"/>
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144 <data name="ReportFile" format="html" label="RepeatExplorer2 - HTML report from data ${FastaFile.hid}"/>
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145 </outputs>
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146
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147 <help>
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148 **HELP**
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149
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150 RepeatExplorer2 clustering is a computational pipeline for unsupervised
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151 identification of repeats from unassembled sequence reads. The
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152 pipeline uses low-pass whole genome sequence reads and performs graph-based
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153 clustering. Resulting clusters, representing all types of repeats, are then
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154 examined to identify and classify into repeats groups.
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155
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156 **Input data**
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157
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158 The analysis requires either **single** or **paired-end reads** generated
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159 by whole genome shotgun sequencing provided as a single fasta-formatted file.
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160 Generally, paired-end reads provide significantly better results than single
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161 reads. Reads should be of uniform length (optimal size range is 100-200 nt) and
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162 the number of analyzed reads should represent less than 1x genome equivalent
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163 (genome coverage of 0.01 - 0.50 x is recommended). Reads should be
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164 quality-filtered (recommended filtering : quality score >=10 over 95% of bases
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165 and no Ns allowed) and only **complete read pairs** should be submitted for
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166 analysis. When paired reads are used, input data must be **interlaced** format
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167 as fasta file:
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168
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169 example of interlaced input format::
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170
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171 >0001_f
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172 CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG
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173 >0001_r
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174 GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT
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175 >0002_f
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176 ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG
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177 >0002_r
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178 TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC
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179 >0003_f
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180 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
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181 >0003_r
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182 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
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183 ...
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184
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185
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186 **Comparative analysis**
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187
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188 For comparative analysis sequence names must contain code (prefix) for each group.
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189 Prefix in sequences names must be of fixed length.
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190
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191 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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192
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193 >AA0001_f
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194 CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG
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195 >AA0001_r
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196 GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT
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197 >AA0002_f
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198 ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG
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199 >AA0002_r
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200 TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC
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201 >BB0001_f
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202 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
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203 >BB0001_r
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204 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
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205 >BB0002_f
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206 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
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207 >BB0002_r
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208 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
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209
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210
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211 To prepare quality filtered and interlaced input fasta file from fastq
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212 files, use `Preprocessing of paired-reads`__ tool.
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213
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214 .. __: tool_runner?tool_id=paired_fastq_filtering
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215
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216
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217 **Additional parameters**
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218
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219 **Sample size** defines how many reads should be used in calculation.
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220 Default setting with 500,000 reads will enable detection of high copy
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221 repeats within several hours of computation time. For higher
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222 sensitivity the sample size can be set higher. Since sample size affects
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223 the memory usage, this parameter may be automatically adjusted to lower
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224 value during the run. Maximum sample size which can be processed depends on
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225 the repetitiveness of analyzed genome.
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226
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227
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228 **Select taxon and protein domain database version (REXdb)**. Classification
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229 of transposable elements is based on the similarity to our reference database
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230 of transposable element protein domains (**REXdb**). Standalone database for Viridiplantae species
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231 can be obtained on `repeatexplorer.org`__. Classification
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232 system used in REXdb is described in article `Systematic survey of plant
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233 LTR-retrotransposons elucidates phylogenetic relationships of their
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234 polyprotein domains and provides a reference for element classification`__
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235 Database for Metazoa species is still under development so use it with caution.
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236
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237 .. __: http://repeatexplorer.org
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238 .. __: https://doi.org/10.1186/s13100-018-0144-1
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239
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240 **Select parameters for protein domain search** REXdb is compared with s
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241 equence clusters either using blastx or diamond aligner. Diamond program
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242 is about three time faster than blastx with word size 3.
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243
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244 **Similarity search options** By default sequence reads are compared using
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245 mgblast program. Default threshold is explicitly set to 90% sequence
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246 similarity spanning at least 55% of the read length (in the case of reads
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247 differing in length it applies to the longer one). Additionally, sequence
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248 overlap must be at least 55 nt. If you select option for shorter reads
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249 than 100 nt, minimum overlap 55 nt is not required.
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250
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251 By default,
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252 mgblast search use DUST program to filter out
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253 low-complexity sequences. If you want
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254 to increase sensitivity of detection of satellites with shorter monomer
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255 use option with '*no masking of low complexity repeats*'. Note that omitting
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256 DUST filtering will significantly increase running times
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257
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258
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259 **Automatic filtering of abundant satellite repeats** perform clustering on
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260 smaller dataset of sequence reads to detect abundant high confidence
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261 satellite repeats. If such satellites are detected, sequence reads derived
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262 from these satellites are depleted from input dataset. This step enable more
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263 sensitive detection of less abundant repeats as more reads can be used
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264 in clustering step.
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265
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266 **Use custom repeat database**. This option allows users to perform similarity
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267 comparison of identified repeats to their custom databases. The repeat class must
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268 be encoded in FASTA headers of database entries in order to allow correct
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269 parsing of similarity hits. Required format for custom database sequence name is: ::
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270
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271 >reapeatname#class/subclass
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272
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273
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274 **Output**
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275
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276 List of clusters identified as putative satellite repeats, their genomic
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277 abundance and various cluster characteristics.
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278
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279 Output includes a **HTML summary** with table listing of all analyzed
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280 clusters. More detailed information about clusters is provided in
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281 additional files and directories. All results are also provided as
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282 downloadable **zip archive**. Additionally a **log file** reporting
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283 the progress of the computational pipeline is provided.
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284
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285 </help>
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286
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287 </tool>
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