Mercurial > repos > iuc > quast

annotate quast.xml @ 13:74be236ac5fd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
author iuc
date Sun, 06 Feb 2022 21:01:58 +0000
parents 83b8464a1931
children 459ceb2ff536
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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1 <tool id="quast" name="Quast" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>Genome assembly Quality</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="bio_tools"/>
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7 <expand macro='requirements' />
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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10 #import re
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bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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12 #if str($in.custom) == 'false'
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13 #set $labels = ','.join( [re.sub('[^\w\-_]', '_', str($x.element_identifier)) for $x in $in.inputs])
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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14 echo $labels &&
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15 #else
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16 #set $labels = []
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17 #for $x in $in.inputs
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18 #if str($x.labels) != ''
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19 #silent $labels.append(re.sub('[^\w\-_]', '_', str($x.labels)))
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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20 #else
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21 #silent $labels.append(re.sub('[^\w\-_]', '_', str($x.input.element_identifier)))
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22 #end if
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23 #end for
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24 #set $labels = ','.join($labels)
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25 #end if
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27 #if $assembly.type == 'metagenome' and $assembly.ref.origin == 'list'
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28 #set $temp_ref_list_fp = 'temp_ref_list_fp'
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29 #set $temp_ref_list_f = open($temp_ref_list_fp, 'w')
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30 #silent $temp_ref_list_f.write('\n'.join([x.strip() for x in $assembly.ref.references_list.split(',')]))
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31 #silent $temp_ref_list_f.close()
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32 #end if
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34 #if $assembly.type == 'genome'
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35 quast
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36 #else
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37 metaquast
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38 #end if
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40 #if $reads.reads_option == 'single'
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41 #for $read in $reads.input_1
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42 --single '$read'
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43 #end for
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44 #else if $reads.reads_option == 'paired'
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45 #for $read in $reads.input_1
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46 --pe1 '$read'
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47 #end for
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48 #for $read in $reads.input_2
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49 --pe2 '$read'
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50 #end for
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51 #else if $reads.reads_option == 'paired_interlaced'
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52 #for $read in $reads.input_1
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53 --pe12 '$read'
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54 #end for
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55 #else if $reads.reads_option == 'mate_paired'
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56 #for $read in $reads.input_1
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57 --mp1 '$read'
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58 #end for
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59 #for $read in $reads.input_2
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60 --mp2 '$read'
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61 #end for
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62 #else if $reads.reads_option == 'pacbio'
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63 #for $read in $reads.input_1
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64 --pacbio '$read'
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65 #end for
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66 #else if $reads.reads_option == 'nanopore'
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67 #for $read in $reads.input_1
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68 --nanopore '$read'
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69 #end for
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70 #end if
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71
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72 --labels $labels
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73 -o outputdir
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74
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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75 #if $assembly.type == 'genome'
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76 #if $assembly.ref.use_ref == 'true'
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77 -r '$assembly.ref.r'
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78 #if $assembly.ref.features
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79 --features '$assembly.ref.features'
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80 #end if
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81 #if $assembly.ref.operons
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82 --operons '$assembly.ref.operons'
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83 #end if
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84 $assembly.ref.circos
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85 $assembly.ref.k_mer.k_mer_stats
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86 #if str($assembly.ref.k_mer.k_mer_stats) != ''
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87 --k-mer-size $assembly.ref.k_mer.k_mer_size
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88 #end if
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89 #else if $assembly.ref.est_ref_size
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90 --est-ref-size $assembly.ref.est_ref_size
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91 #end if
6
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92 $assembly.orga_type
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93 #else
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94 #if $assembly.ref.origin == 'history'
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95 -r '$assembly.ref.r'
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96 #else if $assembly.ref.origin == 'list'
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97 --references-list '$temp_ref_list_fp'
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98 #else if $assembly.ref.origin == 'silva'
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99 --test-no-ref
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100 --max-ref-num '$assembly.ref.max_ref_num'
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101 #end if
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102 #end if
10
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103
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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104 --min-contig $min_contig
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105 $split_scaffolds
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106 $large
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107
6
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108 #if str($genes.gene_finding.tool) != 'none'
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109 $genes.gene_finding.tool
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110 #if $genes.gene_finding.tool == '--gene_finding' or $genes.gene_finding.tool == '--glimmer'
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111 #set $gene_threshold = ','.join([x.strip() for x in str($genes.gene_finding.gene_thresholds).split(',')])
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112 --gene-thresholds '$gene_threshold'
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113 #end if
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114 #end if
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115
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116 $genes.rna_finding
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117 $genes.conserved_genes_finding
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118 $alignments.use_all_alignments
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119 --min-alignment $alignments.min_alignment
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120 --min-identity $alignments.min_identity
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121 --ambiguity-usage '$alignments.ambiguity_usage'
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83b8464a1931 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 0e504686e4ed0ff13e84e4c6b3631a1d1f0bd36f"
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122 --ambiguity-score '$alignments.ambiguity_score'
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123 $alignments.fragmented
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124 $alignments.upper_bound_assembly
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125 #if $alignments.upper_bound_min_con
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126 --upper-bound-min-con $alignments.upper_bound_min_con
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127 #end if
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128
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129 #if $alignments.fragmented
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130 #if $advanced.fragmented_max_indent != ''
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131 --fragmented-max-indent $advanced.fragmented_max_indent
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132 #end if
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133 #end if
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134
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135 #set $contig_thresholds = ','.join([x.strip() for x in str($advanced.contig_thresholds).split(',')])
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136 --contig-thresholds '$contig_thresholds'
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137 $advanced.strict_NA
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138 --extensive-mis-size $advanced.extensive_mis_size
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139 --scaffold-gap-max-size $advanced.scaffold_gap_max_size
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140 --unaligned-part-size $advanced.unaligned_part_size
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141 $advanced.skip_unaligned_mis_contigs
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142
6
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143 #if str($in.custom) == 'false'
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144 #for $k in $in.inputs
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145 '$k'
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146 #end for
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147 #else
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148 #for $k in $in.inputs
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149 '$k.input'
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150 #end for
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151 #end if
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152
10
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153 --threads \${GALAXY_SLOTS:-1}
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154
6
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155 && mkdir -p '$report_html.files_path'
5
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156 && cp outputdir/*.html '$report_html.files_path'
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157
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158 #if ($assembly.type == 'genome' and $assembly.ref.use_ref) or ($assembly.type == 'metagenome' and $assembly.ref.origin != 'none')
5
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159 && cp -R outputdir/icarus_viewers '$report_html.files_path'
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160 #end if
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161
0
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162 ]]>
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163 </command>
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164 <inputs>
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165 <conditional name="in">
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166 <param name="custom" type="select" label="Use customized names for the input files?" help="They will be used in reports, plots and logs">
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167 <option value="true">Yes, specify custom names</option>
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168 <option value="false" selected="true">No, use dataset names</option>
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169 </param>
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170 <when value="true">
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171 <repeat name="inputs" title="Contigs/scaffolds" min="1">
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172 <param name="input" type="data" format="fasta" label="Contigs/scaffolds file"/>
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173 <param argument="--labels" type="text" value="" label="Name"/>
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174 </repeat>
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175 </when>
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176 <when value="false">
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177 <param name="inputs" type="data" format="fasta" multiple="true" label="Contigs/scaffolds file"/>
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178 </when>
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179 </conditional>
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180 <conditional name="reads">
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181 <param name="reads_option" type="select" label="Reads options" help="Currently, the supported read types are Illumina unpaired, paired-end and mate-pair reads, PacBio SMRT, and Oxford Nanopore long reads.">
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182 <option value="disabled">Disabled</option>
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183 <option value="single">Illumina single-end reads</option>
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184 <option value="paired">Illumina paired-end reads</option>
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185 <option value="paired_interlaced">Illumina interlaced paired-end reads</option>
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186 <option value="mate_paired">Illumina mate-pair reads</option>
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187 <option value="pacbio">Pacbio SMRT reads</option>
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188 <option value="nanopore">Nanopore reads</option>
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189 </param>
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190 <when value="disabled"/>
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191
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192 <when value="single">
13
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193 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
10
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194 </when>
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195
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196 <when value="paired">
13
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197 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
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198 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
10
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199 </when>
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200
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201 <when value="paired_interlaced">
13
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202 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
10
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203 </when>
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204
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205 <when value="mate_paired">
13
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206 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
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207 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
10
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208 </when>
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209
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210 <when value="pacbio">
13
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211 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
10
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212 </when>
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213
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214 <when value="nanopore">
13
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215 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
10
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216 </when>
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217 </conditional>
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218
6
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219 <conditional name="assembly">
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220 <param name="type" type="select" label="Type of assembly">
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221 <option value="genome">Genome</option>
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222 <option value="metagenome">Metagenome</option>
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223 </param>
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224 <when value="genome">
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225 <conditional name="ref">
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226 <param name="use_ref" type="select" label="Use a reference genome?" help="Many metrics can't be evaluated without a reference. If this is omitted, QUAST will only report the metrics that can be evaluated without a reference.">
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227 <option value="true">Yes</option>
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228 <option value="false" selected="true">No</option>
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229 </param>
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230 <when value="true">
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231 <param argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" />
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232 <param argument="--features" type="data" format="gff, gff3, bed" optional="true" label="Genomic feature positions in the reference genome" help="Gene coordinates for the reference genome"/>
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233 <param argument="--operons" type="data" format="gff, gff3, bed" optional="true" label="Operon positions in the reference genome" help="Operon coordinates for the reference genome"/>
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234 <conditional name="k_mer">
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235 <param argument="--k-mer-stats" type="select" label="Compute k-mer-based quality metrics?" help="It is recommended for large genomes. This may significantly increase memory and time consumption on large genomes">
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236 <option value="--k-mer-stats">Yes</option>
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237 <option value="" selected="true">No</option>
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238 </param>
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239 <when value="--k-mer-stats">
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240 <param name="k_mer_size" argument="--k-mer-size" type="integer" value="101" label="Size of k" />
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241 </when>
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242 <when value=""/>
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243 </conditional>
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244 <param argument="--circos" type="boolean" truevalue="--circos" falsevalue="" checked="false" label="Generage Circos plot" help="Plot Circos version of Icarus contig alignment viewer"/>
6
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245 </when>
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246 <when value="false">
10
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247 <param argument="--est-ref-size" type="integer" optional="true" label="Estimated reference genome size (in bp) for computing NGx statistics" help=""/>
6
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248 </when>
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249 </conditional>
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250 <param name="orga_type" type="select" label="Type of organism">
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251 <option value="">Prokaryotes: use of GeneMarkS for gene finding (default)</option>
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252 <option value="--eukaryote">Eukaryote: use of GeneMark-ES for gene finding, Barrnap for ribosomal RNA genes prediction, BUSCO for conserved orthologs finding (--eukaryote)</option>
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253 <option value="--fungus">Fungus: use of GeneMark-ES for gene finding, Barrnap for ribosomal RNA genes prediction, BUSCO for conserved orthologs finding (--fungus)</option>
6
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254 </param>
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255 </when>
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256 <when value="metagenome">
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257 <conditional name="ref">
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258 <param name="origin" type="select" label="Reference genome" help="Many metrics can't be evaluated without a reference. If this is omitted, QUAST will only report the metrics that can be evaluated without a reference.">
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259 <option value="history">From history</option>
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260 <option value="list">From list</option>
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261 <option value="silva">From SILVA database</option>
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262 <option value="none" selected="true">None</option>
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263 </param>
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264 <when value="history">
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265 <param argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" />
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266 </when>
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267 <when value="list">
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268 <param name="references_list" argument="references-list" type="text" value="" label="Comma-separated list of reference genomes" help="MetaQUAST will search for these references in the NCBI database and will download the found ones"/>
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269 </when>
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270 <when value="silva">
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271 <param name="max_ref_num" argument="-max-ref-num" type="integer" value="50" label="Maximum number of reference genomes (per each assembly) to download after searching in the SILVA databa" />
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272 </when>
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273 <when value="none"/>
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274 </conditional>
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275 </when>
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276 </conditional>
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277 <param argument="--min-contig" type="integer" value="500" label="Lower threshold for a contig length (in bp)" help="Shorter contigs won't be taken into account"/>
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278 <param argument="--split-scaffolds" type="boolean" truevalue="--split-scaffolds" falsevalue="" checked="false" label="Are assemblies scaffolds rather than contigs?" help="QUAST will add split versions of assemblies to the comparison. Assemblies are split by continuous fragments of N's of length >= 10. If broken version is equal to the original assembly (i.e. nothing was split) it is not included in the comparison."/>
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279 <param argument="--large" type="boolean" truevalue="--large" falsevalue="" checked="false" label="Is genome large (> 100 Mbp)?" help="Use optimal parameters for evaluation of large genomes. Affects speed and accuracy. In particular, imposes --eukaryote --min-contig 3000 --min-alignment 500 --extensive-mis-size 7000 (can be overridden manually with the corresponding options). In addition, this mode tries to identify misassemblies caused by transposable elements and exclude them from the number of misassemblies."/>
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280 <section name="genes" title="Genes">
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281 <conditional name="gene_finding">
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282 <param name="tool" type="select" label="Tool for gene prediction" help="">
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283 <option value="none">Don't predict genes</option>
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284 <option value="--gene-finding">GeneMarkS if prokaryotes or GeneMark-ES if eukaryotes or fungi</option>
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285 <option value="--mgm">MetaGeneMark, specially for metagenomic assembly</option>
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286 <option value="--glimmer">Glimmer</option>
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287 </param>
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288 <when value="none"/>
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289 <when value="--gene-finding">
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290 <expand macro="gene_thresholds"/>
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291 </when>
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292 <when value="--mgm"/>
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293 <when value="--glimmer">
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294 <expand macro="gene_thresholds"/>
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295 </when>
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296 </conditional>
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297 <param argument="--rna-finding" type="boolean" truevalue="--rna-finding" falsevalue="" checked="false" label="Enables ribosomal RNA gene finding?" help="By default, we assume that the genome is prokaryotic, and Barrnap uses the bacterial database for rRNA prediction. If the genome is eukaryotic (fungal), use --eukaryote (--fungus) option to force Barrnap to work with the eukaryotic (fungal) database. "/>
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298 <param argument="--conserved-genes-finding" type="boolean" truevalue="--conserved-genes-finding" falsevalue="" checked="false" label="Enables search for Universal Single-Copy Orthologs using BUSCO?" help="By default, we assume that the genome is prokaryotic, and BUSCO uses the bacterial database of orthologs. If the genome is eukaryotic (fungal), use --eukaryote (--fungus) option to force BUSCO to work with the eukaryotic (fungal) database. "/>
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299 </section>
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300 <section name="alignments" title="Alignments">
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301 <param argument="--use-all-alignments" type="boolean" truevalue="--use-all-alignments" falsevalue="" checked="false" label="Use all alignments as in QUAST v.1.*. to compute genome fraction, # genomic features, # operons metrics?" help="By default, QUAST v.2.0 and higher filters out ambiguous and redundant alignments, keeping only one alignment per contig (or one set of non-overlapping or slightly overlapping alignments)"/>
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302 <param argument="--min-alignment" type="integer" value="65" label="Minimum length of alignment" help="Alignments shorter than this value will be filtered. Note that all alignments shorter than 65 bp will be filtered regardless of this threshold."/>
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303 <param argument="--min-identity" type="float" value="95.0" label="Minimum IDY% considered as proper alignment" help="Alignments with IDY% worse than this value will be filtered. ote that all alignments with IDY% less than 80.0% will be filtered regardless of this threshold. "/>
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304 <param argument="--ambiguity-usage" type="select" label="How processing equally good alignments of a contig (probably repeats)?" help="">
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305 <option value="none">Skip all such alignments</option>
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306 <option value="one" selected="true">Take only one (the very best one)</option>
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307 <option value="all">Use all alignments. It can cause a significant increase of # mismatches (repeats are almost always inexact due to accumulated SNPs, indels, etc.). It is useful for metagenomic assemblies where ambiguous alignments might represent homologous sequences of different strains</option>
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308 </param>
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309 <param argument="--ambiguity-score" type="float" value="0.99" min="0.8" max="1.0" label="Score S for defining equally good alignments of a single contig" help="All alignments are sorted by decreasing LEN × IDY% value. All alignments with LEN × IDY% less than S × best(LEN × IDY%) are discarded. "/>
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310 <param argument="--fragmented" type="boolean" truevalue="--fragmented" falsevalue="" checked="false" label="Fragmented reference genome" help="Reference genome is fragmented (e.g. a scaffold reference). QUAST will try to detect misassemblies caused by the fragmentation and mark them fake (will be excluded from misassemblies). Note: QUAST will not detect misassemblies caused by the linear representation of circular genome "/>
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311 <param argument="--upper-bound-assembly" type="boolean" truevalue="--upper-bound-assembly" falsevalue="" label="Simulate upper bound assembly" help="Simulate upper bound assembly based on the reference genome and a given set reads (mate-pairs or long reads, such as Pacbio SMRT/Oxford Nanopore, are REQUIRED). This assembly is added to the comparison and could be useful for estimating the upper bounds of completeness and contiguity that theoretically can be reached by assembly software from this particular set of reads. The concept is based on the fact that the reference genome cannot be completely reconstructed from raw reads due to long genomic repeats and low covered regions." />
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312 <param argument="--upper-bound-min-con" type="integer" value="" optional="true" label="Minimal number of 'connecting reads' needed for joining upper bound contigs into a scaffold" help="This is important for a realistic estimation of genome assembly fragmentation due to long repeats. The default values is 2 for mate-pairs and 1 for long reads (PacBio or Nanopore libraries)"/>
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313 </section>
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314 <section name="advanced" title="Advanced options">
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315 <param argument="--contig-thresholds" type="text" value="0,1000" label="Comma-separated list of contig length thresholds (in bp)" help="Used in # contigs ≥ x and total length (≥ x) metrics"/>
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316 <param argument="--strict-NA" type="boolean" truevalue="--strict-NA" falsevalue="" checked="false" label="Break contigs at every misassembly event (including local ones) to compute NAx and NGAx statistics?" help="By default, QUAST breaks contigs only at extensive misassemblies (not local ones)."/>
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317 <param argument="--extensive-mis-size" type="integer" value="1000" min="85" label="Lower threshold for the relocation size (gap or overlap size between left and right flanking sequence)" help="Shorter relocations are considered as local misassemblies. It does not affect other types of extensive misassemblies (inversions and translocations). The default value is 1000 bp. Note that the threshold should be greater than maximum indel length which is 85 bp."/>
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318 <param argument="--scaffold-gap-max-size" type="integer" value="1000" label="Max allowed scaffold gap length difference for detecting corresponding type of misassemblies" help="Longer inconsistencies are considered as relocations and thus, counted as extensive misassemblies. The default value is 10000 bp. Note that the threshold make sense only if it is greater than extensive misassembly size"/>
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319 <param argument="--unaligned-part-size" type="integer" value="500" label="Lower threshold for detecting partially unaligned contigs" help=""/>
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320 <param argument="--skip-unaligned-mis-contigs" type="boolean" truevalue="" falsevalue="--skip-unaligned-mis-contigs" checked="true" label="Distinguish contigs with more than 50% unaligned bases as a separate group of contigs?" help="By default, QUAST breaks contigs only at extensive misassemblies (not local ones)."/>
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321 <param argument="--fragmented-max-indent" type="integer" min="0" value="" optional="true" label="Fragment max indent" help="Mark translocation as fake if both alignments are located no further than N bases from the ends of the reference fragments. The value should be less than extensive misassembly size.Default value is 50. Note: requires --fragmented option" />
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322 </section>
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323 <param name="output_files" type="select" display="checkboxes" optional="true" multiple="true" label="Output files">
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324 <option value="html" selected="true">HTML report</option>
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325 <option value="pdf">PDF report</option>
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326 <option value="tabular">Tabular reports</option>
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327 <option value="log">Log file</option>
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328 </param>
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329 </inputs>
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330 <outputs>
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331 <data name="quast_tabular" format="tabular" label="${tool.name} on ${on_string}: tabular report" from_work_dir="outputdir/report.tsv">
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332 <filter>'tabular' in output_files</filter>
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333 </data>
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334 <data name="report_html" format="html" label="${tool.name} on ${on_string}: HTML report" from_work_dir="outputdir/report.html">
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335 <filter>'html' in output_files</filter>
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336 </data>
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337 <data name="report_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF report" from_work_dir="outputdir/report.pdf">
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338 <filter>'pdf' in output_files</filter>
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339 </data>
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340 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outputdir/quast.log">
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341 <filter>'log' in output_files</filter>
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342 </data>
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343 <data name="mis_ass" format="tabular" label="${tool.name} on ${on_string}: Misassemblies report" from_work_dir="outputdir/contigs_reports/misassemblies_report.txt">
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344 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true'</filter>
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345 <filter>'tabular' in output_files</filter>
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346 </data>
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347 <data name="unalign" format="tabular" label="${tool.name} on ${on_string}: Unaligned contigs report" from_work_dir="outputdir/contigs_reports/unaligned_report.tsv">
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348 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true'</filter>
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349 <filter>'tabular' in output_files</filter>
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350 </data>
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351 <data name="kmers" format="tabular" label="${tool.name} on ${on_string}: K-mer-based metrics report" from_work_dir="outputdir/k_mer_stats/kmers_report.txt">
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352 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true' and assembly['ref']['k_mer']['k_mer_stats'] != ''</filter>
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353 <filter>'tabular' in output_files</filter>
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354 </data>
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355 <data name="circos_output" format="png" from_work_dir="outputdir/circos/circos.png" label="${tool.name} on ${on_string}: Circos plot">
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356 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true' and assembly['ref']['circos']</filter>
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357 </data>
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358 </outputs>
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359 <tests>
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360 <!-- Test 01: reference, genes annotations and operon coordinates -->
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361 <test expect_num_outputs="2">
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362 <conditional name="in">
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363 <param name="custom" value="true"/>
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364 <repeat name="inputs">
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365 <param name="input" value="contigs1.fna"/>
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366 <param name="labels" value="contig1"/>
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367 </repeat>
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368 <repeat name="inputs">
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369 <param name="input" value="contigs2.fna"/>
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370 <param name="labels" value="contig2"/>
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371 </repeat>
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372 </conditional>
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373 <conditional name="assembly">
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374 <param name="type" value="genome"/>
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375 <conditional name="ref">
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376 <param name="use_ref" value="true"/>
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377 <param name="r" value="reference.fna"/>
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378 <param name="features" value="genes.gff"/>
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379 <param name="operons" value="operons.bed"/>
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380 <conditional name="k_mer">
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381 <param name="k_mer_stats" value="--k-mer-stats"/>
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382 <param name="k_mer_size" value="101" />
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383 </conditional>
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384 <param name="circos" value="true"/>
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385 </conditional>
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386 <param name="orga_type" value=""/>
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387 </conditional>
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388 <param name="min_contig" value="500"/>
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389 <param name="split_scaffolds" value="false"/>
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390 <section name="genes">
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391 <conditional name="gene_finding">
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392 <param name="tool" value="--gene_finding"/>
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393 <param name="gene_thresholds" value="0,300,1500,3000"/>
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394 </conditional>
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395 <param name="rna_finding" value="true"/>
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396 <param name="conserved_genes_finding" value="true"/>
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397 </section>
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398 <section name="alignments">
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399 <param name="use_all_alignments" value="true"/>
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400 <param name="min_alignment" value="65"/>
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401 <param name="min_identity" value="95.0"/>
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402 <param name="ambiguity_usage" value="one"/>
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403 <param name="ambiguity_score" value="0.99"/>
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404 </section>
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405 <section name="advanced">
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406 <param name="contig_thresholds" value="0,1000"/>
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407 <param name="strict_NA" value="true"/>
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408 <param name="extensive_mis_size" value="1000"/>
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409 <param name="scaffold_gap_max_size" value="1000"/>
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410 <param name="unaligned_part_size" value="500"/>
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411 <param name="skip_unaligned_mis_contigs" value="true"/>
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412 <param name="fragmented_max_indent" value="50"/>
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413 </section>
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414 <param name="output_files" value="html"/>
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415 <output name="report_html" file="test1_report.html" ftype="html" compare="sim_size"/>
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416 <output name="circos_output" file="test1_circos.png" ftype="png" compare="sim_size"/>
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417 </test>
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418 <!-- Test 02: all outputs -->
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419 <test expect_num_outputs="8">
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420 <conditional name="in">
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421 <param name="custom" value="true"/>
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422 <repeat name="inputs">
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423 <param name="input" value="contigs1.fna"/>
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424 <param name="labels" value="contig1"/>
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425 </repeat>
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426 <repeat name="inputs">
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427 <param name="input" value="contigs2.fna"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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428 <param name="labels" value="contig2"/>
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429 </repeat>
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430 </conditional>
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431 <conditional name="assembly">
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432 <param name="type" value="genome"/>
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433 <conditional name="ref">
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434 <param name="use_ref" value="true"/>
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435 <param name="r" value="reference.fna"/>
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436 <param name="features" value="genes.gff"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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437 <param name="operons" value="operons.bed"/>
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438 <conditional name="k_mer">
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439 <param name="k_mer_stats" value="--k-mer-stats"/>
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440 <param name="k_mer_size" value="101" />
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441 </conditional>
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442 <param name="circos" value="true"/>
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443 </conditional>
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444 </conditional>
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445 <param name="output_files" value="html,pdf,tabular,log"/>
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446 <output name="report_html" file="test2_report.html" ftype="html" compare="sim_size"/>
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447 <output name="report_pdf" file="test2_report.pdf" ftype="pdf" compare="sim_size"/>
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448 <output name="quast_tabular" file="test2_report.tab" ftype="tabular"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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449 <output name="log" file="test2.log" ftype="txt" compare="sim_size"/>
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450 <output name="mis_ass" file="test2_missasemblies.tab" ftype="tabular"/>
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451 <output name="unalign" file="test2_unaligned.tab" ftype="tabular"/>
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452 <output name="kmers" file="test2_kmers.tab" ftype="tabular"/>
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453 <output name="circos_output" file="test2_circos.png" ftype="png" compare="sim_size"/>
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454 </test>
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455 <!-- Test 03: without reference -->
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456 <test expect_num_outputs="3">
6
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457 <conditional name="in">
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458 <param name="custom" value="false"/>
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459 <param name="inputs" value="contigs1.fna,contigs2.fna"/>
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460 </conditional>
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iuc
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461 <conditional name="assembly">
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iuc
parents: 5
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462 <param name="type" value="genome"/>
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463 <conditional name="ref">
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464 <param name="use_ref" value="false"/>
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465 </conditional>
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466 <param name="orga_type" value="--eukaryote"/>
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467 </conditional>
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parents: 5
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468 <param name="min_contig" value="500"/>
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469 <param name="split_scaffolds" value="false"/>
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470 <param name="large" value="false"/>
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471 <section name="genes">
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472 <conditional name="gene_finding">
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473 <param name="tool" value="none"/>
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474 </conditional>
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parents: 5
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475 <param name="rna_finding" value="false"/>
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iuc
parents: 5
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476 <param name="conserved_genes_finding" value="false"/>
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477 </section>
10
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478 <section name="alignments">
6
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479 <param name="use_all_alignments" value="false"/>
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parents: 5
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480 <param name="min_alignment" value="65"/>
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481 <param name="min_identity" value="95.0"/>
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482 <param name="ambiguity_usage" value="one"/>
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483 <param name="ambiguity_score" value="0.99"/>
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parents: 5
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484 <param name="fragmented" value="false"/>
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485 </section>
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486 <section name="advanced">
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487 <param name="contig_thresholds" value="0,1000, 500"/>
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488 <param name="strict_NA" value="false"/>
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489 <param name="extensive_mis_size" value="1000"/>
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490 <param name="scaffold_gap_max_size" value="1000"/>
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491 <param name="unaligned_part_size" value="500"/>
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492 <param name="skip_unaligned_mis_contigs" value="-"/>
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493 </section>
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494 <param name="output_files" value="html,pdf,log" />
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495 <output name="log" file="test3.log" ftype="txt" compare="sim_size"/>
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496 <output name="report_html" file="test3_report.html" compare="sim_size"/>
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497 <output name="report_pdf" file="test3_report.pdf" compare="sim_size"/>
3
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498 </test>
10
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499 <!-- Test 04: metagenomics -->
6
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500 <test>
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501 <conditional name="in">
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502 <param name="custom" value="false"/>
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503 <param name="inputs" value="contigs3.fasta"/>
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504 </conditional>
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505 <conditional name="assembly">
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506 <param name="type" value="metagenome"/>
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507 <conditional name="ref">
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508 <param name="origin" value="none"/>
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509 </conditional>
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510 </conditional>
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511 <param name="min_contig" value="500"/>
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512 <param name="split_scaffolds" value="false"/>
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513 <param name="large" value="false"/>
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514 <section name="genes">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
515 <conditional name="gene_finding">
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
516 <param name="tool" value="--mgm"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
517 </conditional>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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diff changeset
518 <param name="rna_finding" value="false"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
519 <param name="conserved_genes_finding" value="false"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
520 </section>
10
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diff changeset
521 <section name="alignments">
6
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
522 <param name="use_all_alignments" value="false"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
523 <param name="min_alignment" value="65"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
524 <param name="min_identity" value="95.0"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
525 <param name="ambiguity_usage" value="one"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
526 <param name="ambiguity_score" value="0.99"/>
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
527 <param name="fragmented" value="false"/>
10
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 9
diff changeset
528 </section>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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diff changeset
529 <section name="advanced">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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diff changeset
530 <param name="contig_thresholds" value="0,1000, 500"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
531 <param name="strict_NA" value="false"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
532 <param name="extensive_mis_size" value="1000"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
533 <param name="scaffold_gap_max_size" value="1000"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
534 <param name="unaligned_part_size" value="500"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
535 <param name="skip_unaligned_mis_contigs" value="-"/>
6
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
536 </section>
10
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
537 <param name="output_files" value="tabular"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
538 <output name="quast_tabular" file="test4.tab" ftype="tabular"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
539 </test>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
540 <!-- Test 05: FASTQ read files -->
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
541 <test expect_num_outputs="3">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
542 <conditional name="in">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
543 <param name="custom" value="true"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
544 <repeat name="inputs">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
545 <param name="input" value="contigs1.fna"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
546 <param name="labels" value="contig1"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
547 </repeat>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
548 <repeat name="inputs">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
549 <param name="input" value="contigs2.fna"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
550 <param name="labels" value="contig2"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
551 </repeat>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
552 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
553 <conditional name="reads">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
554 <param name="reads_option" value="pacbio"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
555 <param name="input_1" value="pacbio_01.fastq,pacbio_02.fastq,pacbio_03.fastq,pacbio_04.fastq"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
556 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
557 <conditional name="assembly">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
558 <param name="type" value="genome"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
559 <conditional name="ref">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
560 <param name="use_ref" value="true"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
561 <param name="r" value="reference.fna"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
562 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
563 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
564 <section name="alignments">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
565 <param name="upper_bound_assembly" value="true"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
566 <param name="upper_bound_min_con" value="1"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
567 </section>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
568 <param name="output_files" value="tabular"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
569 <output name="quast_tabular" file="test5.tab" ftype="tabular"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
570 <output name="mis_ass" file="test5_missasemblies.tab" ftype="tabular"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
571 <output name="unalign" file="test5_unaligned.tab" ftype="tabular"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
572 </test>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
573 <!-- Test 6: FASTQ.gz read files -->
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
574 <test expect_num_outputs="1">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
575 <conditional name="in">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
576 <param name="custom" value="true"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
577 <repeat name="inputs">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
578 <param name="input" value="contigs1.fna"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
579 <param name="labels" value="contig1"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
580 </repeat>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
581 <repeat name="inputs">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
582 <param name="input" value="contigs2.fna"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
583 <param name="labels" value="contig2"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
584 </repeat>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
585 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
586 <conditional name="reads">
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
587 <param name="reads_option" value="single"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
588 <param name="input_1" value="pacbio_01.fastq.gz,pacbio_02.fastq.gz"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
589 </conditional>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
590 <param name="output_files" value="tabular"/>
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 9
diff changeset
591 <output name="quast_tabular" file="test6.tab" ftype="tabular"/>
6
bf2c7b30dfb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
592 </test>
13
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 12
diff changeset
593 <!-- Test 7: FASTA.gz read files -->
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 12
diff changeset
594 <test expect_num_outputs="1">
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 12
diff changeset
595 <conditional name="in">
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 12
diff changeset
596 <param name="custom" value="true"/>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 12
diff changeset
597 <repeat name="inputs">
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 12
diff changeset
598 <param name="input" value="contigs1.fna"/>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 12
diff changeset
599 <param name="labels" value="contig1"/>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 12
diff changeset
600 </repeat>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 12
diff changeset
601 <repeat name="inputs">
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 12
diff changeset
602 <param name="input" value="contigs2.fna"/>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 12
diff changeset
603 <param name="labels" value="contig2"/>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 12
diff changeset
604 </repeat>
74be236ac5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 12
diff changeset
605 </conditional>
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606 <conditional name="reads">
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607 <param name="reads_option" value="single"/>
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608 <param name="input_1" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>
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609 </conditional>
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610 <param name="output_files" value="tabular"/>
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611 <output name="quast_tabular" file="test7.tab" ftype="tabular"/>
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612 </test>
0
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613 </tests>
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614 <help>
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615 <![CDATA[
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616 **What it does**
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617
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618 QUAST = QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics.
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619
8
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620 If you have one or multiple genome assemblies, you can assess their quality with Quast. It works with or without reference genome. If you are new to Quast, start by reading its `manual page <http://quast.sourceforge.net/docs/manual.html>`_.
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621
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622 **Using Quast without reference**
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623
4
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624 Without reference Quast can calculate a number of assembly related-metrics but cannot provide any information about potential misassemblies, inversions, translocations, etc. Suppose you have three assemblies produced by Unicycler corresponding to three different antibiotic treatments *car*, *pit*, and *cef* (these stand for carbenicillin, piperacillin, and cefsulodin, respectively). Evaluating them without reference will produce the following Quast outputs:
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625
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626 * Quast report in HTML format
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627 * `Contig viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)
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628 * `Quast report <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_ in Tab-delimited format
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629 * Quast log (a file technical information about Quast tool execution)
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630
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631 The **tab delimited Quast report** will contain the following information::
0
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632
4
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633 Assembly pit_fna cef_fna car_fna
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634 # contigs (>= 0 bp) 100 91 94
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635 # contigs (>= 1000 bp) 62 58 61
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636 Total length (>= 0 bp) 6480635 6481216 6480271
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637 Total length (>= 1000 bp) 6466917 6468946 6467103
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638 # contigs 71 66 70
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639 Largest contig 848753 848766 662053
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640 Total length 6473173 6474698 6473810
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641 GC (%) 66.33 66.33 66.33
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642 N50 270269 289027 254671
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643 N75 136321 136321 146521
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644 L50 7 7 8
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645 L75 15 15 16
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646 # N's per 100 kbp 0.00 0.00 0.00
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647
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648 where values are defined as specified in `Quast manual <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_
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649
4
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650 **Quast report in HTML format** contains graphs in addition to the above metrics, while **Contig viewer** draws contigs ordered from longest to shortest. This ordering is suitable for comparing only largest contigs or number of contigs longer than a specific threshold. The viewer shows N50 and N75 with color and textual indication. If the reference genome is available or at least approximate genome length is known (see `--est-ref-size`), NG50 and NG75 are also shown. You can also tone down contigs shorter than a specified threshold using Icarus control panel:
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651
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652 .. image:: $PATH_TO_IMAGES/contig_view_noR.png
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653 :width: 558
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654 :height: 412
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655
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656 Also see `Plot description <http://quast.sourceforge.net/docs/manual.html#sec2>`_ section of the manual.
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657
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658 **Using Quast with reference**
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659
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660 Car, pit, and cef are in fact assemblies of *Pseudomonas aeruginosa* UCBPP-PA14, so we can use its genome as a reference (by supplying a Fasta file containing *P. aeruginosa* pa14 genome to **Reference genome** input box). The following outputs will be produced (note the alignment viewer):
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661
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662 * Quast report in HTML format
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663 * `Contig viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)
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664 * `Alignment viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)
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665 * `Quast report <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_ in Tab-delimited format
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666 * Summary of `misassemblies <http://quast.sourceforge.net/docs/manual.html#sec3.1.2>`_
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667 * Summary of `unaligned contigs <http://quast.sourceforge.net/docs/manual.html#sec3.1.3>`_
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668 * Quast log (a file technical information about Quast tool execution)
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669
4
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670 With the reference Quast produces a much more comprehensive set of results::
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671
4
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672 Assembly pit_fna cef_fna car_fna
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673 # contigs (>= 0 bp) 100 91 94
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674 # contigs (>= 1000 bp) 62 58 61
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675 Total length (>= 0 bp) 6480635 6481216 6480271
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676 Total length (>= 1000 bp) 6466917 6468946 6467103
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677 # contigs 71 66 70
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678 Largest contig 848753 848766 662053
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679 Total length 6473173 6474698 6473810
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680 Reference length 6537648 6537648 6537648
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681 GC (%) 66.33 66.33 66.33
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682 Reference GC (%) 66.29 66.29 66.29
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683 N50 270269 289027 254671
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684 NG50 270269 289027 254671
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685 N75 136321 136321 146521
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686 NG75 136321 136321 136321
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687 L50 7 7 8
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688 LG50 7 7 8
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689 L75 15 15 16
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690 LG75 15 15 17
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691 # misassemblies 0 0 0
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692 # misassembled contigs 0 0 0
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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693 Misassembled contigs length 0 0 0
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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694 # local misassemblies 1 1 2
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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695 # unaligned mis. contigs 0 0 0
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
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696 # unaligned contigs 0 + 0 0 + 0 0 + 0
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
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697 part part part
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
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698 Unaligned length 0 0 0
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
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699 Genome fraction (%) 99.015 99.038 99.025
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
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700 Duplication ratio 1.000 1.000 1.000
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
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701 # N's per 100 kbp 0.00 0.00 0.00
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
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702 # mismatches per 100 kbp 3.82 3.63 3.49
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
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703 # indels per 100 kbp 1.19 1.13 1.13
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
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704 Largest alignment 848753 848766 662053
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
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705 Total aligned length 6473163 6474660 6473792
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
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706 NA50 270269 289027 254671
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
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707 NGA50 270269 289027 254671
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
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708 NA75 136321 136321 146521
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
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709 NGA75 136321 136321 136321
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
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710 LA50 7 7 8
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
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711 LGA50 7 7 8
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
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712 LA75 15 15 16
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4c2bef52f68e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents: 7
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713 LGA75 15 15 17
0
350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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714
8
4c2bef52f68e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
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715 where, again, values are defined as specified in `Quast manual <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_. You can see that this report includes a variety of data that can only be computer against a reference assembly.
4
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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716
10
e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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717 Using reference also produces an **Alignment viewer**:
4
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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parents: 3
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718
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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719 .. image:: $PATH_TO_IMAGES/Align_view.png
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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parents: 3
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720 :width: 515
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
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721 :height: 395
d90201633fb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
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722
8
4c2bef52f68e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
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723 Alignment viewer highlights regions of interest as, in this case, missassemblies that can potentially point to genome rearrangements (see more `here <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_).
0
350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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724
350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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725 ]]>
350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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726 </help>
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e377f054bcd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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727 <expand macro="citations"/>
0
350257634bbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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728 </tool>