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annotate rna_quast.xml @ 7:3125faf00ffd draft

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planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
author iuc
date Fri, 30 Aug 2024 13:23:03 +0000
parents 8e66f695d859
children f73ab5187eed
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1 <tool id="rna_quast" name="rnaQUAST" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>A quality assessment tool for De Novo transcriptome assemblies</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro='xrefs'/>
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7 <expand macro='requirements'/>
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8 <stdio>
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9 <regex match="Traceback " source="both" level="fatal" description="rnaQuast failed" />
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10 </stdio>
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11 <command detect_errors="exit_code"><![CDATA[
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12 mkdir -p './complete_reports/' &&
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13 mkdir -p './fasta_files/' &&
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14 #import os, re, glob
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15 #for $i in $transcripts
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16 ln -s '$i' '${re.sub('[^\w.]', '_', i.element_identifier)}' &&
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17 #end for
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18 #if $reference
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19 #for $rf in $reference
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20 ln -s '$rf' '${re.sub('[^\w.]', '_', rf.element_identifier)}' &&
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21 #end for
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22 #end if
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23 #if $gene_coordinates.selector == "true"
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24 #for $g in $gene_coordinates.gtf
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25 ln -s '$g' '${re.sub('[^\w.]', '_', g.element_identifier)}' &&
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26 #end for
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27 #end if
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28 mkdir outputdir &&
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29 rnaQUAST.py
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30 --threads \${GALAXY_SLOTS:-8}
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31 --transcripts
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32 #for $i in $transcripts
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33 '${re.sub('[^\w.]', '_', i.element_identifier)}'
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34 #end for
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35 #if $reads_option.selector == 'paired'
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36 --left_reads '${reads_option.forward_reads}'
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37 --right_reads '${reads_option.reverse_reads}'
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38 #else if $reads_option.selector == 'single'
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39 --single_reads '${reads_option.single_reads}'
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40 #end if
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41 $advanced_options.strand_specific
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42 #if $reads_alignment
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43 --reads_alignment '${reads_alignment}'
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44 #end if
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45 #if $reference
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46 -r
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47 #for $rf in $reference
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48 '${re.sub('[^\w.]', '_', rf.element_identifier)}'
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49 #end for
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50 #end if
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51 #if $gene_coordinates.selector == "true"
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52 --gtf
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53 #for $g in $gene_coordinates.gtf
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54 '${re.sub('[^\w.]', '_', g.element_identifier)}'
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55 #end for
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56 $gene_coordinates.disable_infer_genes
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57 $gene_coordinates.disable_infer_transcripts
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58 #end if
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59 $advanced_options.prokaryote
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60 --min_alignment $advanced_options.min_alignment
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61 $advanced_options.blat
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62
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63 #if "pdf" not in $output_options.out_sr
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64 --no_plots
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65 #end if
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66 #if $use_busco.selector == 'true'
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67 --busco
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68 #if $use_busco.lineage_conditional.selector == 'cached':
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69 '${use_busco.lineage_conditional.cached_db.fields.path}'
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70 #else
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71 $use_busco.lineage
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72 #end if
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73 #end if
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74 ## $advanced_options.gene_mark
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75 $advanced_options.meta
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76 --lower_threshold $advanced_options.lower_threshold
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77 --upper_threshold $advanced_options.upper_threshold
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78 -o outputdir
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79
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80 #if 'gz' in $output_options.out_add
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81 && tar -czvf results.tar.gz './outputdir'
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82 #end if
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83
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84 #if len($transcripts) == 1
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85 #set $path = "/".join(['outputdir',re.sub('[^\w.]', '_', $transcripts[0].element_identifier).split(".")[0]]) + "_output"
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86 && mv '${path}' './results'
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87 ## rename .list files to .txt files to make them detectable
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88 && find './results/' -name "*.list" -exec mv {} {}.txt \;
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89 && true
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90 && printf "************ METRICS/TRANSCRIPTS ***************\n" > stats.txt
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91 && for file_name in ./results/*txt; do printf "\n************ \$file_name ************\n" >> stats.txt
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92 && sed 's/^ ==.*/&\n/' \$file_name | tail -q -n +2 "\$file_name" >> stats.txt;
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93 done
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94 && cat stats.txt > $stats
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95 #if $gene_coordinates.selector == 'true' and $reference
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96 && mv ./results/*fasta ./fasta_files/
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97 #end if
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98 #else
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99 && mkdir -p './results/'
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100 #if $gene_coordinates.selector == 'true' and $reference
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101 #for $i, $transcript in enumerate($transcripts)
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102 #set $path = "/".join(['outputdir',re.sub('[^\w.]', '_', $transcripts[$i].element_identifier).split(".")[0]]) + "_output"
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103 && rm -r ./results
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104 && cp -r $path './results'
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105 && mv ./results/*fasta './fasta_files/'
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106 #end for
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107 #end if
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108 && find './outputdir/comparison_output' -name "*.list" -exec mv {} {}.txt \;
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109 && true
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110 && printf "************ COMPARISON METRICS ***************\n" > stats.txt
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111 && for file_name in ./outputdir/comparison_output/*txt; do printf "\n************ \$file_name ************\n" >> stats.txt
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112 && sed 's/^ ==.*/&\n/' \$file_name | tail -q -n +2 "\$file_name" >> stats.txt; done
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113 && cat stats.txt > $stats
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114 #end if
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115 ]]> </command>
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116 <inputs>
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117 <param argument="--transcripts" type="data" format="fasta" multiple="true" label="Transcripts" help="File(s) with transcripts in FASTA format."/>
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118 <conditional name="reads_option">
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119 <param name="selector" type="select" label="Single-end or paired-end reads">
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120 <option value="" selected="true">Disabled-end</option>
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121 <option value="single" selected="true">Single-end</option>
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122 <option value="paired">Paired-end (as individual datasets)</option>
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123 </param>
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124 <when value=""/>
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125 <when value="single">
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126 <param format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" name="single_reads" type="data" label="RNA-Seq FASTQ/FASTA file"/>
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127 </when>
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128 <when value="paired">
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129 <param name="forward_reads" format="fastq,fastq.gz,fastqsanger ,fastqsanger.gz" type="data" label="RNA-Seq FASTQ/FASTA file, forward reads"/>
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130 <param name="reverse_reads" format="fastq,fastq.gz,fastqsanger, fastqsanger.gz" type="data" label="RNA-Seq FASTQ/FASTA file, reverse reads"/>
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131 </when>
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132 </conditional>
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133 <param argument="--reference" type="data" format="fasta" label="Reference genome" multiple="true" optional="true" help="File with reference genome containing all chromosomes/scaffolds in FASTA forma." />
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134 <conditional name="gene_coordinates">
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135 <param name="selector" type="select" label="Genome annotation" help="Genome annotation file. We recommend to use files downloaded from GENCODE or Ensembl.">
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136 <option value="true">Enabled</option>
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137 <option value="false" selected="true">Disabled</option>
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138 </param>
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139 <when value="true">
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140 <param argument="--gtf" type="data" format="gtf,gff,gff3" multiple="true" label="GTF/GFF file" />
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141 <param argument="--disable_infer_genes" type="boolean" truevalue="--disable_infer_genes" falsevalue="" checked="false" label=" Disable infer genes"
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142 help="Use this option if your GTF file already contains genes records, otherwise gffutils will fix it. Note that gffutils may work for quite a long time"/>
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143 <param argument="--disable_infer_transcripts" type="boolean" truevalue="--disable_infer_transcripts" falsevalue="" checked="false" label="Disable infer transcripts" help="Is option if your GTF file already contains transcripts records, otherwise gffutils will fix it."/>
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144 </when>
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145 <when value="false">
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146 </when>
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147 </conditional>
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148 <param argument="--reads_alignment" type="data" format="sam" label="Aligned reads to reference genome" optional="true" help="File with read alignments to the reference genome" />
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149 <conditional name="use_busco">
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150 <param argument="selector" type="select" label="Run BUSCO" help="BUSCO allows to detect core genes in the assembled transcripts">
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151 <option value="false">Disabled</option>
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152 <option value="true">Enabled</option>
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153 </param>
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154 <when value="false"/>
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155 <when value="true">
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156 <conditional name="lineage_conditional">
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157 <param name="selector" type="select" label="Lineage data source">
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158 <option value="download">Download lineage data</option>
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159 <option value="cached" selected="true">Use cached lineage data</option>
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160 </param>
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161 <when value="cached">
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162 <param name="cached_db" label="Cached database with lineage" type="select">
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163 <options from_data_table="busco_database">
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164 <validator message="No BUSCO database is available" type="no_options" />
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165 </options>
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166 </param>
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167 </when>
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168 <when value="download">
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169 <param name="lineage" type="select" label="Lineage" help="Select a lineage for using BUSCO">
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170 <option value="metazoa">Metazoa</option>
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171 <option value="eukaryota">Eukaryota</option>
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172 <option value="arthropoda">Arthropoda</option>
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173 <option value="vertebrata">Vertebrata</option>
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174 <option value="fungi">Fungi</option>
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175 <option value="bacteria">Bacteria</option>
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176 </param>
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177 </when>
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178 </conditional>
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179 </when>
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180 </conditional>
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181 <section name="advanced_options" title="Advaced options" >
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182 <param name="strand_specific" argument="-ss" type="boolean" truevalue="-ss" falsevalue="" checked="false" label="Strand-specific RNA-seq data"
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183 help="Set if transcripts were assembled using strand-specific RNA-Seq data in order to benefit from knowing whether the transcript originated from the + or - strand"/>
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184 <param argument="--min_alignment" type="integer" min="0" value="50" label="Minimal alignment length to be used" help="Default value is 50"/>
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185 <param argument="--blat" type="boolean" truevalue="--blat" falsevalue="" checked="false" label="Run with BLAT instead of GMAP" help="BALT is especially useful for aligning long sequences and gapped mapping, which cannot be performed properly by other fast sequence mappers designed for short reads. " />
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186 <!-- GeneMarkST is not in Bioconda -->
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187 <!--param argument="-\-gene_mark" type="boolean" truevalue="-\-gene_mark" falsevalue="" checked="false" label="Run with GeneMarkS-T gene prediction tool?"
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188 help="GeneMarkS-T allows to predict genes in the assembled transcripts without reference genome"/-->
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189 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="false" label="Meta Transcriptome" help="Run quality asessment for meta-transcriptome assemblies" />
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190 <param argument="--lower_threshold" type="integer" value="50" label="Lower threshold for x-assembled/covered/matched metrics." />
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191 <param argument="--upper_threshold" type="integer" value="95" label="Upper threshold for x-assembled/covered/matched metrics." />
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192 <param argument="--prokaryote" type="boolean" truevalue="--prokaryote" falsevalue="" checked="false" label="Prokararyotic organism(s)" help="Use this option if the genome is prokaryotic"/>
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193 </section>
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194 <section name="output_options" title="Output options" expanded="true">
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195 <param name="out_sr" type="select" multiple="true" display="checkboxes" label="Short report formats">
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196 <option value="tabular">Tabular</option>
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197 <option value="tex">TeX</option>
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198 <option value="pdf" selected="true">PDF</option>
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199 </param>
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200 <param name="out_add" type="select" label="Additional outputs" multiple="true" display="checkboxes">
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201 <option value="complete">Complete report</option>
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202 <option value="fasta" >FASTA files</option>
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203 <option value="logs">Logs</option>
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204 <option value="gz">Compressed output folder</option>
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205 </param>
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206 </section>
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207 </inputs>
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208 <outputs>
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209 <data name="stats" format="txt" label="${tool.name} on ${on_string}: complete report">
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210 <filter>output_options['out_add'] and "complete" in output_options['out_add']</filter>
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211 </data>
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212 <collection name="list_logs" type="list" label="${tool.name} on ${on_string}: logs">
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213 <discover_datasets ext="txt" pattern="(?P&lt;name&gt;.+)\.log" directory="outputdir/logs" visible="false" />
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214 <filter>output_options['out_add'] and "logs" in output_options['out_add']</filter>
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215 </collection>
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216 <collection name="fasta_files" type="list" label="${tool.name} on ${on_string}: FASTA files">
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217 <discover_datasets ext="fasta" pattern="(?P&lt;name&gt;.+)\.fasta" directory="fasta_files" visible="false" />
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218 <filter>output_options['out_add'] and "fasta" in output_options['out_add']</filter>
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219 <filter>gene_coordinates['selector'] == 'true'</filter>
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220 <filter>reference</filter>
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221 </collection>
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222 <data name="compressed_files" format="tgz" label="${tool.name} on ${on_string}: compressed results folder" from_work_dir="results.tar.gz">
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223 <filter>output_options['out_add'] and "gz" in output_options['out_add']</filter>
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224 </data>
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225 <data name="short_report_pdf" format="pdf" label="${tool.name} on ${on_string}: short report (pdf)" from_work_dir="outputdir/short_report.pdf">
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226 <filter>output_options['out_sr'] and "pdf" in output_options['out_sr']</filter>
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227 </data>
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228 <data name="short_report_tex" format="txt" label="${tool.name} on ${on_string}: short report (tex)" from_work_dir="outputdir/short_report.tex">
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229 <filter>output_options['out_sr'] and "tex" in output_options['out_sr']</filter>
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230 </data>
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231 <data name="short_report_tabular" format="tabular" label="${tool.name} on ${on_string}: short report (tabular)" from_work_dir="outputdir/short_report.tsv">
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232 <filter>output_options['out_sr'] and "tabular" in output_options['out_sr']</filter>
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233 </data>
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234 </outputs>
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235 <tests>
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236 <!-- Test 01: Minimum input txt output-->
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237 <test expect_num_outputs="1">
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238 <param name="transcripts" value="transcriptome01.fasta"/>
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239 <section name="output_options">
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240 <param name="out_sr" value="tabular"/>
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241 </section>
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242 <output name="short_report_tabular" file="test_01_short_report.tab"/>
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243 </test>
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244 <!-- Test 02: Transcriptome reference,single read, txt output-->
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245 <test expect_num_outputs="1">
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246 <param name="transcripts" value="transcriptome01.fasta"/>
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247 <section name="output_options">
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248 <param name="out_sr" value="tabular"/>
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249 </section>
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250 <conditional name="reads_option">
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251 <param name="selector" value="single"/>
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252 <param name="single_reads" value="single_end.fastq.gz"/>
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253 </conditional>
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254 <output name="short_report_tabular">
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255 <assert_contents>
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256 <has_text text="Transcripts" />
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257 <has_size value="95" delta="5"/>
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258 </assert_contents>
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259 </output>
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260 </test>
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261 <!-- Test 03: Transcriptome reference and annotation, txt output-->
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262 <test expect_num_outputs="1">
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263 <param name="transcripts" value="transcriptome01.fasta"/>
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264 <conditional name="gene_coordinates">
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265 <param name="selector" value="true"/>
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266 <param name="gtf" value="reference.gtf"/>
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267 </conditional>
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268 <section name="output_options">
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269 <param name="out_sr" value="tabular"/>
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270 </section>
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271 <conditional name="reads_option">
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272 <param name="selector" value="single"/>
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273 <param name="single_reads" value=""/>
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274 </conditional>
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275 <output name="short_report_tabular" file="test_03_short_report.tab"/>
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276 </test>
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277 <!-- Test 04: Transcriptome reference and annotation, txt output-->
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278 <test expect_num_outputs="1">
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279 <param name="transcripts" value="transcriptome01.fasta"/>
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280 <conditional name="gene_coordinates">
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281 <param name="selector" value="true"/>
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282 <param name="gtf" value="reference.gtf"/>
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283 </conditional>
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284 <section name="output_options">
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285 <param name="out_sr" value="tabular"/>
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286 </section>
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287 <conditional name="reads_option">
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288 <param name="selector" value="single"/>
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289 <param name="single_reads" value="single_end.fastq.gz"/>
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290 </conditional>
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291 <output name="short_report_tabular">
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292 <assert_contents>
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293 <has_text text="Transcripts" />
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294 <has_size value="140" delta="5"/>
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295 </assert_contents>
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296 </output>
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297 </test>
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298 <!-- Test 05: Transcriptome reference, annotation and mapping, txt output-->
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299 <test expect_num_outputs="1">
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300 <param name="transcripts" value="transcriptome01.fasta"/>
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301 <conditional name="gene_coordinates">
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302 <param name="selector" value="true"/>
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303 <param name="gtf" value="reference.gtf"/>
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304 </conditional>
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305 <section name="output_options">
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306 <param name="out_sr" value="tabular"/>
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307 </section>
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308 <conditional name="reads_option">
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309 <param name="selector" value='paired'/>
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310 <param name="forward_reads" value="input_F.fastqsanger"/>
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311 <param name="reverse_reads" value="input_F.fastqsanger"/>
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312 </conditional>
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313 <output name="short_report_tabular">
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314 <assert_contents>
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315 <has_text text="Transcripts" />
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316 <has_size value="140" delta="5"/>
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317 </assert_contents>
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318 </output>
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319 </test>
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320 <!-- Test 06: Transcriptome reference, annotation, mapping and BUSCO, txt output-->
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321 <test expect_num_outputs="1">
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322 <param name="transcripts" value="transcriptome01.fasta"/>
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323 <conditional name="gene_coordinates">
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324 <param name="selector" value="true"/>
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325 <param name="gtf" value="reference.gtf"/>
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326 </conditional>
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327 <conditional name="reads_option">
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328 <param name="selector" value='paired'/>
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329 <param name="forward_reads" value="input_F.fastqsanger"/>
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330 <param name="reverse_reads" value="input_R.fastqsanger"/>
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331 </conditional>
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332 <section name="output_options">
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333 <param name="out_sr" value="tabular"/>
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334 </section>
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335 <conditional name="use_busco">
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336 <param name="selector" value="true"/>
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337 <conditional name="lineage_conditional">
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338 <param name="selector" value="cached"/>
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339 <param name="cached_db" value="busco-demo-db-20230328"/>
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340 </conditional>
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341 </conditional>
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342 <output name="short_report_tabular">
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343 <assert_contents>
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344 <has_text text="Transcripts" />
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345 <has_size value="140" delta="5"/>
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346 </assert_contents>
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347 </output>
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348 </test>
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349 <!-- Test 07: Transcriptome reference, annotation, mapping and BUSCO, additional outputs-->
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350 <test expect_num_outputs="4">
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351 <param name="transcripts" value="transcriptome01.fasta"/>
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352 <conditional name="gene_coordinates">
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353 <param name="selector" value="true"/>
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354 <param name="gtf" value="reference.gtf"/>
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355 </conditional>
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356 <param name="reference" value="reference.fasta"/>
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357 <conditional name="reads_option">
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358 <param name="selector" value='paired'/>
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359 <param name="forward_reads" value="input_F.fastqsanger"/>
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360 <param name="reverse_reads" value="input_R.fastqsanger"/>
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361 </conditional>
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362 <conditional name="use_busco">
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363 <param name="selector" value="true"/>
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364 <conditional name="lineage_conditional">
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365 <param name="selector" value="cached"/>
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366 <param name="cached_db" value="busco-demo-db-20230328"/>
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367 </conditional>
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368 </conditional>
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369 <section name="output_options">
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370 <param name="out_sr" value="pdf,tabular"/>
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371 <param name="out_add" value="fasta,gz"/>
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372 </section>
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373 <output_collection name="fasta_files" type="list" count="7">
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374 <element name="transcriptome01.paralogs" file="test_07_paralogs.fasta" ftype="fasta"/>
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375 </output_collection>
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376 <output name="short_report_pdf" file="test_07_short_report.pdf" ftype="pdf" compare="sim_size" delta="1000"/>
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377 <output name="short_report_tabular" file="test_07_short_report.tab" ftype="tabular"/>
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378 <output name="compressed_files" ftype="tgz">
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379 <assert_contents>
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380 <has_archive_member path="./outputdir/.*" n="62" delta="0"/>
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381 <has_archive_member path="./outputdir/logs/.*" n="10" delta="0"/>
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382 <has_archive_member path="./outputdir/transcriptome01_output/.*" n="45" delta="0"/>
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383 </assert_contents>
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384 </output>
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385 </test>
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386 <!-- Test 08: Multiple inputs-->
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387 <test expect_num_outputs="6">
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388 <param name="transcripts" value="transcriptome01.fasta,transcriptome?02.fasta"/>
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389 <param name="reference" value="reference.fasta"/>
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390 <conditional name="gene_coordinates">
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391 <param name="selector" value="true"/>
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392 <param name="gtf" value="reference.gtf"/>
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393 </conditional>
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394 <section name="output_options">
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395 <param name="out_sr" value="tabular,pdf"/>
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396 </section>
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397 <conditional name="use_busco">
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398 <param name="selector" value="true"/>
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399 <conditional name="lineage_conditional">
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400 <param name="selector" value="cached"/>
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401 <param name="cached_db" value="busco-demo-db-20230328"/>
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402 </conditional>
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403 </conditional>
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404 <param name="out_add" value="complete,fasta,logs,gz"/>
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405 <conditional name="reads_option">
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406 <param name="selector" value="single"/>
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407 <param name="single_reads" value="single_end.fastq.gz"/>
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408 </conditional>
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409 <output name="short_report_tabular" value="test_08_short_report.tab" ftype="tabular"/>
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410 <output name="short_report_pdf" value="test_08_short_report.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/>
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411 <output name="stats" value="test_08_complete_report.tab" ftype="txt" lines_diff="6" />
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412 <output_collection name="fasta_files" type="list" count="14">
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413 <element name="transcriptome01.paralogs" file="test_08_paralogs.fasta" ftype="fasta"/>
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414 </output_collection>
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415 <output_collection name="list_logs" type="list" count="14">
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416 <element name="STAR.out" ftype="txt">
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417 <assert_contents>
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418 <has_text text="STAR --runThreadN"/>
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419 <has_text text="finished successfully"/>
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420 </assert_contents>
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421 </element>
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422 <element name="gmap_build.out" ftype="txt">
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423 <assert_contents>
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424 <has_text text="No alternate scaffolds observed"/>
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425 </assert_contents>
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426 </element>
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427 <element name="rnaQUAST" ftype="txt">
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428 <assert_contents>
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429 <has_text text="THE QUALITY OF TRANSCRIPTOME ASSEMBLY DONE"/>
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430 <has_text text="Thank you for using rnaQUAST!"/>
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431 </assert_contents>
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432 </element>
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433 </output_collection>
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434 </test>
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435 <!-- Test 09: Multiple inputs with dash in names-->
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436 <test expect_num_outputs="6">
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437 <param name="transcripts" value="transcriptome01.fasta,transcriptome-02.fasta"/>
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438 <param name="reference" value="reference.fasta"/>
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439 <conditional name="gene_coordinates">
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440 <param name="selector" value="true"/>
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441 <param name="gtf" value="reference.gtf"/>
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442 </conditional>
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443 <section name="output_options">
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444 <param name="out_sr" value="tabular,pdf"/>
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445 </section>
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446 <conditional name="use_busco">
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447 <param name="selector" value="true"/>
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448 <conditional name="lineage_conditional">
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449 <param name="selector" value="cached"/>
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450 <param name="cached_db" value="busco-demo-db-20230328"/>
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451 </conditional>
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452 </conditional>
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453 <param name="out_add" value="complete,fasta,logs,gz"/>
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454 <conditional name="reads_option">
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455 <param name="selector" value="single"/>
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456 <param name="single_reads" value="single_end.fastq.gz"/>
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457 </conditional>
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458 <output name="short_report_tabular" value="test_08_short_report.tab" ftype="tabular"/>
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459 <output name="short_report_pdf" value="test_08_short_report.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/>
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460 <output name="stats" value="test_08_complete_report.tab" ftype="txt" lines_diff="6" />
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461 <output_collection name="fasta_files" type="list" count="14">
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462 <element name="transcriptome01.paralogs" file="test_08_paralogs.fasta" ftype="fasta"/>
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463 </output_collection>
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464 <output_collection name="list_logs" type="list" count="14">
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465 <element name="STAR.out" ftype="txt">
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466 <assert_contents>
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467 <has_text text="STAR --runThreadN"/>
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468 <has_text text="finished successfully"/>
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469 </assert_contents>
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470 </element>
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471 <element name="gmap_build.out" ftype="txt">
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472 <assert_contents>
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473 <has_text text="No alternate scaffolds observed"/>
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474 </assert_contents>
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475 </element>
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476 <element name="rnaQUAST" ftype="txt">
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477 <assert_contents>
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478 <has_text text="THE QUALITY OF TRANSCRIPTOME ASSEMBLY DONE"/>
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479 <has_text text="Thank you for using rnaQUAST!"/>
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480 </assert_contents>
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481 </element>
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482 </output_collection>
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483 </test>
0
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484 </tests>
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485 <help><![CDATA[
5
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486
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487 .. class:: infomark
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488
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489 **Purpose**
0
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490
5
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491 rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable
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492 of estimating gene database coverage by raw reads and de novo quality assessment.
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493
5
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494 .. class:: infomark
0
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495
5
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496 **rnaQUAST pipeline**
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497
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498 To evaluate quality of the assembled transcripts, rnaQUAST takes a reference genome in FASTA format and optionally its gene database in
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499 GFF/GTF format. A user can provide either a FASTA file with transcripts, which will be aligned to the given reference genome using GMAP
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500 or BLAT. The alignments are analyzed to calculate simple metrics and then are matched against the isoforms from the gene database in order
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
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501 to obtain statistics that represent completeness and correctness levels of the assembly. In addition, rnaQUAST is capable of estimating
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
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502 gene database coverage by raw reads using STAR or TopHat2. For de novo quality assessment when reference genome and gene database are
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503 unavailable, the transcripts are analyzed using BUSCO.
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504
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505 .. class:: infomark
0
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506
5
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507 **Metrics and alignment analysis**
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508
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509 rnaQUAST calculates various metrics without using alignment information, e.g. length distribution and N50 of the assembled transcripts.
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510 Additionally, rnaQUAST computes the following statistics for the gene database: the total number of genes and isoforms, isoform and exon
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511 length distribution, average number of exons per gene, etc.
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512
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513 To analyze transcripts' alignments, rnaQUAST firstly filters out short partial alignments (shorter than a user-defined threshold, default
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514 value is 50 bp). Such short alignments are typically caused by genomic repeats and thus are ignored. Afterwards, rnaQUAST selects the
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515 best-scored spliced alignment for each transcript. If a transcript has more than one alignment with the highest score, it is reported
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516 as multiply aligned. Otherwise, it is considered to be uniquely aligned. If the best-scored alignment is discordant (e.g. the transcript
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517 has partial alignments that are either mapped to different strands or to different chromosomes) the transcript is classified as misassembled.
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518 Transcripts without misassemblies are analyzed to calculate such metrics as average transcript alignment fraction and mismatch rate.
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519
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520 For the simplicity of explanation, transcript is further referred to as a sequence generated by the assembler and isoform denotes a sequence
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521 from the gene database. rnaQUAST matches best-scored alignments of non-misassembled transcripts to the isoforms' coordinates and analyzes
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522 them to estimate how well the isoforms are covered by the assembly. rnaQUAST computes such metrics as database coverage (the total number
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523 of covered bases of all isoforms divided by the total length of all isoforms) and the number of 50%/95%-assembled isoforms. An isoform is
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524 considered to be x%-assembled if it has at least x% covered by a single transcript. Vice versa, to evaluate how well the assembled
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525 transcripts are covered by the isoforms, rnaQUAST estimates the number of unannotated transcripts (that align to the genome, but do not
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526 match to any isoform) and the number of 50%/95%-matched transcripts (that have corresponding fraction mapped to an isoform). Indeed, the
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527 thresholds described above (50% and 95%) can be varied by the user.
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528
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529
1
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530 ]]> </help>
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531 <citations>
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532 <citation type="doi">10.1093/bioinformatics/btw218 </citation>
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533 </citations>
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534 </tool>