annotate quast.xml @ 14:3061c8b029e5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
author iuc
date Fri, 05 Aug 2022 15:21:27 +0000
parents 675488238c96
children 72472698a2df
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1 <tool id="quast" name="Quast" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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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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11 #import os
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13 #if str($in.custom) == 'false'
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14 #set $labels = ','.join( [re.sub('[^\w\-_]', '_', str($x.element_identifier)) for $x in $in.inputs])
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15 echo $labels &&
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16 #else
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17 #set $labels = []
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18 #for $x in $in.inputs
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19 #if str($x.labels) != ''
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20 #silent $labels.append(re.sub('[^\w\-_]', '_', str($x.labels)))
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21 #else
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22 #silent $labels.append(re.sub('[^\w\-_]', '_', str($x.input.element_identifier)))
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23 #end if
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24 #end for
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25 #set $labels = ','.join($labels)
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26 #end if
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28 #if $assembly.type == 'metagenome' and $assembly.ref.origin == 'list'
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29 #set $temp_ref_list_fp = 'temp_ref_list'
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30 #for $i in $assembly.ref.references_list.split(',')
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31 echo $i >> $temp_ref_list_fp &&
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32 #end for
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33 #end if
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35 #if $reads.reads_option == 'paired'
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36 #for $read in $reads.input_1
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37 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
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38 ln -s '$read' 'pe1-${identifier}.${read.ext}' &&
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39 #end for
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40 #for $read in $reads.input_2
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41 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
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42 ln -s '$read' 'pe2-${identifier}.${read.ext}' &&
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43 #end for
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44 #else if $reads.reads_option == 'paired_collection'
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45 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($reads.input_1.element_identifier))
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46 ln -s '$reads.input_1.forward' 'pe1-${identifier}.${reads.input_1.forward.ext}' &&
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47 ln -s '$reads.input_1.reverse' 'pe2-${identifier}.${reads.input_1.reverse.ext}' &&
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48 #end if
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49
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50 #if $assembly.type == 'genome'
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51 quast
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52 #else
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53 metaquast
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54 #end if
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55
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56 #if $reads.reads_option == 'single'
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57 #for $read in $reads.input_1
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58 --single '$read'
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59 #end for
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60 #else if $reads.reads_option == 'paired'
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61 #for $read in $reads.input_1
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62 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
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63 --pe1 'pe1-${identifier}.${read.ext}'
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64 #end for
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65 #for $read in $reads.input_2
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66 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
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67 --pe2 'pe2-${identifier}.${read.ext}'
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68 #end for
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69 #else if $reads.reads_option == 'paired_collection'
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70 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($reads.input_1.element_identifier))
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71 --pe1 'pe1-${identifier}.${reads.input_1.forward.ext}'
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72 --pe2 'pe2-${identifier}.${reads.input_1.reverse.ext}'
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73 #else if $reads.reads_option == 'paired_interlaced'
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74 #for $read in $reads.input_1
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75 --pe12 '$read'
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76 #end for
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77 #else if $reads.reads_option == 'mate_paired'
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78 #for $read in $reads.input_1
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79 --mp1 '$read'
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80 #end for
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81 #for $read in $reads.input_2
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82 --mp2 '$read'
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83 #end for
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84 #else if $reads.reads_option == 'pacbio'
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85 #for $read in $reads.input_1
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86 --pacbio '$read'
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87 #end for
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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88 #else if $reads.reads_option == 'nanopore'
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89 #for $read in $reads.input_1
14
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iuc
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90 --nanopore '$read'
9
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91 #end for
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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92 #end if
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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93
14
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iuc
parents: 13
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94 --labels '$labels'
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iuc
parents: 13
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95 -o 'outputdir'
6
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96
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iuc
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97 #if $assembly.type == 'genome'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
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98 #if $assembly.ref.use_ref == 'true'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
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99 -r '$assembly.ref.r'
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
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100 #if $assembly.ref.features
14
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101 --features '$assembly.ref.features'
6
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102 #end if
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iuc
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103 #if $assembly.ref.operons
14
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104 --operons '$assembly.ref.operons'
9
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iuc
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105 #end if
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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diff changeset
106 $assembly.ref.circos
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107 $assembly.ref.k_mer.k_mer_stats
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108 #if str($assembly.ref.k_mer.k_mer_stats) != ''
14
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109 --k-mer-size $assembly.ref.k_mer.k_mer_size
6
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110 #end if
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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111 #else if $assembly.ref.est_ref_size
14
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iuc
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112 --est-ref-size $assembly.ref.est_ref_size
5
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iuc
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113 #end if
6
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114 $assembly.orga_type
14
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115 #else if $assembly.type == 'metagenome'
6
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116 #if $assembly.ref.origin == 'history'
14
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117 -r '$assembly.ref.r'
6
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118 #else if $assembly.ref.origin == 'list'
14
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119 --references-list '$temp_ref_list_fp'
6
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120 #else if $assembly.ref.origin == 'silva'
14
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121 --test-no-ref
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iuc
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122 --max-ref-num $assembly.ref.max_ref_num
5
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iuc
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123 #end if
14
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iuc
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124 $assembly.reuse_combined_alignments
5
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125 #end if
9
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126
14
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iuc
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127 --min-identity $assembly.min_identity
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128
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iuc
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129 --min-contig $min_contig
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iuc
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130 $split_scaffolds
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131 $large
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132
6
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133 #if str($genes.gene_finding.tool) != 'none'
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134 $genes.gene_finding.tool
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135 #if $genes.gene_finding.tool == '--gene_finding' or $genes.gene_finding.tool == '--glimmer'
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136 #set $gene_threshold = ','.join([x.strip() for x in str($genes.gene_finding.gene_thresholds).split(',')])
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iuc
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137 --gene-thresholds '$gene_threshold'
6
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138 #end if
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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139 #end if
9
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140
14
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141 $genes.rna_finding
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142 $genes.conserved_genes_finding
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iuc
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143 $alignments.use_all_alignments
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iuc
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144 --min-alignment $alignments.min_alignment
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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145 --ambiguity-usage '$alignments.ambiguity_usage'
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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146 --ambiguity-score $alignments.ambiguity_score
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iuc
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147 $alignments.fragmented
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148 $alignments.upper_bound_assembly
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149 #if $alignments.upper_bound_min_con
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150 --upper-bound-min-con $alignments.upper_bound_min_con
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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151 #end if
14
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diff changeset
152 #if $alignments.local_mis_size
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iuc
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153 --local-mis-size $alignments.local_mis_size
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154 #end if
9
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155
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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156 #if $alignments.fragmented
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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157 #if $advanced.fragmented_max_indent != ''
14
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iuc
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158 --fragmented-max-indent $advanced.fragmented_max_indent
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159 #end if
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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160 #end if
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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161
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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diff changeset
162 #set $contig_thresholds = ','.join([x.strip() for x in str($advanced.contig_thresholds).split(',')])
14
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163 --contig-thresholds '$contig_thresholds'
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iuc
parents: 13
diff changeset
164 $advanced.strict_NA
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iuc
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diff changeset
165 --extensive-mis-size $advanced.extensive_mis_size
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iuc
parents: 13
diff changeset
166 --scaffold-gap-max-size $advanced.scaffold_gap_max_size
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
167 --unaligned-part-size $advanced.unaligned_part_size
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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diff changeset
168 $advanced.skip_unaligned_mis_contigs
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iuc
parents: 13
diff changeset
169 $advanced.report_all_metrics
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iuc
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diff changeset
170 --x-for-Nx $advanced.x_for_Nx
3
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parents: 2
diff changeset
171
6
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diff changeset
172 #if str($in.custom) == 'false'
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173 #for $k in $in.inputs
14
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diff changeset
174 '$k'
6
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diff changeset
175 #end for
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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diff changeset
176 #else
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177 #for $k in $in.inputs
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178 '$k.input'
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179 #end for
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180 #end if
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181 --threads \${GALAXY_SLOTS:-1}
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182
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183 #if $assembly.type == 'genome'
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184 && mkdir -p '$report_html.files_path'
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185 && cp outputdir/*.html '$report_html.files_path'
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186 #if $assembly.ref.use_ref
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187 && cp -R outputdir/icarus_viewers '$report_html.files_path'
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188 #end if
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189 #else
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190 && if [[ -f "outputdir/report.tsv" ]]; then mkdir -p "outputdir/combined_reference/" && cp "outputdir/report.tsv" "outputdir/combined_reference/report.tsv"; fi
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191 && if [[ -f "outputdir/report.html" ]]; then mkdir -p "outputdir/combined_reference/" && cp outputdir/*.html "outputdir/combined_reference/"; fi
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192 && mkdir -p '$report_html_meta.files_path'
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193 && cp outputdir/combined_reference/*.html '$report_html_meta.files_path'
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194 && if [[ -d "outputdir/icarus_viewers" ]]; then cp -R outputdir/icarus_viewers 'outputdir/combined_reference/'; fi
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195 && if [[ -d "outputdir/combined_reference/icarus_viewers" ]]; then cp -R outputdir/combined_reference/icarus_viewers '$report_html_meta.files_path'; fi
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196 && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p '$krona.files_path' && cp outputdir/krona_charts/*.html '$krona.files_path'; fi
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197 #end if
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198 ]]></command>
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199 <inputs>
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200 <conditional name="in">
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201 <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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202 <option value="true">Yes, specify custom names</option>
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203 <option value="false" selected="true">No, use dataset names</option>
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204 </param>
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205 <when value="true">
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206 <repeat name="inputs" title="Contigs/scaffolds" min="1">
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207 <param name="input" type="data" format="fasta" label="Contigs/scaffolds file"/>
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208 <param argument="--labels" type="text" value="" label="Name"/>
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209 </repeat>
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210 </when>
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211 <when value="false">
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212 <param name="inputs" type="data" format="fasta" multiple="true" label="Contigs/scaffolds file"/>
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213 </when>
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214 </conditional>
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215 <conditional name="reads">
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216 <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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217 <option value="disabled">Disabled</option>
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218 <option value="single">Illumina single-end reads</option>
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219 <option value="paired">Illumina paired-end reads</option>
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220 <option value="paired_collection">Illumina paired-end reads in paired collection</option>
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221 <option value="paired_interlaced">Illumina interlaced paired-end reads</option>
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222 <option value="mate_paired">Illumina mate-pair reads</option>
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223 <option value="pacbio">Pacbio SMRT reads</option>
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224 <option value="nanopore">Nanopore reads</option>
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225 </param>
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226 <when value="disabled"/>
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227 <when value="single">
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228 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
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229 </when>
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230 <when value="paired">
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231 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
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232 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
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233 </when>
14
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234 <when value="paired_collection">
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235 <param name="input_1" type="data_collection" collection_type="paired" format="fastq,fastq.gz,fasta,fasta.gz" label="FASTQ/FASTA files" />
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236 </when>
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237 <when value="paired_interlaced">
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238 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
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239 </when>
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240 <when value="mate_paired">
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241 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
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242 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
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243 </when>
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244 <when value="pacbio">
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245 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
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246 </when>
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247 <when value="nanopore">
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248 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
9
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249 </when>
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250 </conditional>
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251 <conditional name="assembly">
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252 <param name="type" type="select" label="Type of assembly">
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253 <option value="genome">Genome</option>
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254 <option value="metagenome">Metagenome</option>
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255 </param>
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256 <when value="genome">
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257 <conditional name="ref">
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258 <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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259 <option value="true">Yes</option>
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260 <option value="false" selected="true">No</option>
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261 </param>
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262 <when value="true">
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263 <param argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" />
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264 <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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265 <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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266 <conditional name="k_mer">
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267 <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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268 <option value="--k-mer-stats">Yes</option>
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269 <option value="" selected="true">No</option>
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270 </param>
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271 <when value="--k-mer-stats">
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272 <param name="k_mer_size" argument="--k-mer-size" type="integer" value="101" label="Size of k" />
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273 </when>
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274 <when value=""/>
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275 </conditional>
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276 <param argument="--circos" type="boolean" truevalue="--circos" falsevalue="" checked="false" label="Generage Circos plot" help="Plot Circos version of Icarus contig alignment viewer"/>
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277 </when>
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278 <when value="false">
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279 <param argument="--est-ref-size" type="integer" optional="true" label="Estimated reference genome size (in bp) for computing NGx statistics" help=""/>
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280 </when>
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281 </conditional>
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282 <param name="orga_type" type="select" label="Type of organism">
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283 <option value="">Prokaryotes: use of GeneMarkS for gene finding (default)</option>
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284 <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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285 <option value="--fungus">Fungus: use of GeneMark-ES for gene finding, Barrnap for ribosomal RNA genes prediction, BUSCO for conserved orthologs finding (--fungus)</option>
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286 </param>
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287 <expand macro="min_identity_macros" value="95"/>
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288 </when>
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289 <when value="metagenome">
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290 <conditional name="ref">
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291 <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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292 <option value="history">From history</option>
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293 <option value="list">From list</option>
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294 <option value="silva">From SILVA database</option>
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295 <option value="none" selected="true">None</option>
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296 </param>
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297 <when value="history">
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298 <param argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" />
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299 </when>
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300 <when value="list">
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301 <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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302 </when>
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303 <when value="silva">
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304 <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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305 </when>
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306 <when value="none"/>
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307 </conditional>
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308 <param argument="--reuse-combined-alignments" type="boolean" truevalue="--reuse-combined-alignments" falsevalue="" checked="false" label="Reuse the alignments on the combined reference" help="Reuse the alignments on the combined reference in the subsequent runs per separate references. That is, the alignment procedure is performed only once (for all assemblies against the combined reference) and does NOT executed for each subgroups of contigs against the corresponding separate reference genomes. In each separate reference run, all precomputed assembly alignments for other references are simply ignored" />
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309 <expand macro="min_identity_macros" value="90"/>
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310 </when>
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311 </conditional>
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312 <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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313 <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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314 <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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315 <section name="genes" title="Genes">
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316 <conditional name="gene_finding">
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317 <param name="tool" type="select" label="Tool for gene prediction" help="">
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318 <option value="none">Don't predict genes</option>
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319 <option value="--gene-finding">GeneMarkS if prokaryotes or GeneMark-ES if eukaryotes or fungi</option>
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320 <option value="--mgm">MetaGeneMark, specially for metagenomic assembly</option>
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321 <option value="--glimmer">Glimmer</option>
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322 </param>
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323 <when value="none"/>
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324 <when value="--gene-finding">
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325 <expand macro="gene_thresholds"/>
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326 </when>
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327 <when value="--mgm"/>
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328 <when value="--glimmer">
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329 <expand macro="gene_thresholds"/>
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330 </when>
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331 </conditional>
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332 <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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333 <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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334 </section>
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335 <section name="alignments" title="Alignments">
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336 <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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337 <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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338 <param argument="--ambiguity-usage" type="select" label="How processing equally good alignments of a contig (probably repeats)?" help="">
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339 <option value="none">Skip all such alignments</option>
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340 <option value="one" selected="true">Take only one (the very best one)</option>
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341 <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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342 </param>
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343 <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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344 <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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345 <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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346 <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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347 <param argument="--local-mis-size" type="integer" value="200" optional="true" label="Minimal local misassembly size" help="Lower threshold for the local misassembly size. Shorter inconsistencies are considered as (long) indels. The default value is 200 bp. Note that the threshold should be equal to or lower than minimal extensive misassembly size, which is 1000 bp by default"/>
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348 </section>
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349 <section name="advanced" title="Advanced options">
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350 <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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351 <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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352 <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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353 <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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354 <param argument="--unaligned-part-size" type="integer" value="500" label="Lower threshold for detecting partially unaligned contigs" help=""/>
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355 <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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356 <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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357 <param argument="--report-all-metrics" type="boolean" truevalue="--report-all-metrics" falsevalue="" checked="false" label="Report all metrics" help="Keep all quality metrics in the main report. Usually, all not-relevant metrics are not included in the report, e.g., reference-based metrics in the no-reference mode. Also, if metric values are undefined for all input assemblies, the metric is removed from the report" />
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358 <param argument="--x-for-Nx" type="integer" min="0" max="100" value="90" label="Report Nx, Lx, etc metrics for specific value of 'x'" help="Value of 'x' for Nx, Lx, NGx, NGAx, etc metrics reported in addition to N50, L50, NG50, NGA50, etc" />
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359 </section>
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360 <param name="output_files" type="select" display="checkboxes" optional="true" multiple="true" label="Output files">
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361 <option value="html" selected="true">HTML reports</option>
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362 <option value="pdf">PDF reports</option>
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363 <option value="tabular">Tabular reports</option>
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364 <option value="log">Log file</option>
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365 <option value="summary">Key metric summary (metagenome mode)</option>
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366 <option value="krona">Krona charts (metagenome mode without reference genomes)</option>
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367 </param>
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368 </inputs>
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369 <outputs>
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370 <data name="report_tabular" format="tabular" label="${tool.name} on ${on_string}: tabular report" from_work_dir="outputdir/report.tsv">
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371 <filter>assembly['type'] == 'genome' and 'tabular' in output_files</filter>
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372 </data>
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373 <data name="report_tabular_meta" format="tabular" label="${tool.name} on ${on_string}: tabular report for combined reference genome" from_work_dir="outputdir/combined_reference/report.tsv">
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374 <filter>assembly['type'] == 'metagenome' and 'tabular' in output_files</filter>
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375 </data>
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376 <data name="report_html" format="html" label="${tool.name} on ${on_string}: HTML report" from_work_dir="outputdir/report.html">
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377 <filter>assembly['type'] == 'genome' and 'html' in output_files</filter>
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378 </data>
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379 <data name="report_html_meta" format="html" label="${tool.name} on ${on_string}: HTML report for combined reference genome" from_work_dir="outputdir/combined_reference/report.html">
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380 <filter>assembly['type'] == 'metagenome' and 'html' in output_files</filter>
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381 </data>
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382 <data name="report_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF report" from_work_dir="outputdir/report.pdf">
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383 <filter>assembly['type'] == 'genome' and 'pdf' in output_files</filter>
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384 </data>
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385 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outputdir/quast.log">
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386 <filter>assembly['type'] == 'genome' and 'log' in output_files</filter>
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387 </data>
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388 <data name="log_meta" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outputdir/metaquast.log">
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389 <filter>assembly['type'] == 'metagenome' and 'log' in output_files</filter>
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390 </data>
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391 <data name="mis_ass" format="tabular" label="${tool.name} on ${on_string}: Misassemblies report" from_work_dir="outputdir/contigs_reports/misassemblies_report.txt">
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392 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true'</filter>
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393 <filter>'tabular' in output_files</filter>
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394 </data>
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395 <data name="unalign" format="tabular" label="${tool.name} on ${on_string}: Unaligned contigs report" from_work_dir="outputdir/contigs_reports/unaligned_report.tsv">
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396 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true'</filter>
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397 <filter>'tabular' in output_files</filter>
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398 </data>
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399 <data name="kmers" format="tabular" label="${tool.name} on ${on_string}: K-mer-based metrics report" from_work_dir="outputdir/k_mer_stats/kmers_report.txt">
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400 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true' and assembly['ref']['k_mer']['k_mer_stats'] != ''</filter>
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401 <filter>'tabular' in output_files</filter>
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402 </data>
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403 <data name="circos_output" format="png" from_work_dir="outputdir/circos/circos.png" label="${tool.name} on ${on_string}: Circos plot">
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404 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true' and assembly['ref']['circos']</filter>
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405 </data>
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406 <collection name="metrics_tabular" type="list" label="${tool.name} on ${on_string}: Tabular reports for key metrics" >
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407 <discover_datasets pattern="(?P&lt;designation&gt;.+).tsv" directory="outputdir/summary/TSV/" format="tabular"/>
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408 <filter>assembly['type'] == 'metagenome' and 'summary' in output_files</filter>
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409 </collection>
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410 <collection name="metrics_pdf" type="list" label="${tool.name} on ${on_string}: PDF reports for key metrics" >
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411 <discover_datasets pattern="(?P&lt;designation&gt;.+).pdf" directory="outputdir/summary/PDF/" format="pdf"/>
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412 <filter>assembly['type'] == 'metagenome' and 'summary' in output_files</filter>
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413 </collection>
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414 <data name="krona" format="html" label="${tool.name} on ${on_string}: Krona chart" from_work_dir="outputdir/krona_charts/*.html">
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415 <filter>assembly['type'] == 'metagenome' and assembly['ref']['origin'] == 'none' and 'krona' in output_files</filter>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
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416 </data>
0
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417 </outputs>
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418 <tests>
9
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419 <!-- Test 01: reference, genes annotations and operon coordinates -->
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420 <test expect_num_outputs="2">
6
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421 <conditional name="in">
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422 <param name="custom" value="true"/>
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423 <repeat name="inputs">
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parents: 5
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424 <param name="input" value="contigs1.fna"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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425 <param name="labels" value="contig1"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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426 </repeat>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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427 <repeat name="inputs">
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428 <param name="input" value="contigs2.fna"/>
9
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429 <param name="labels" value="contig2"/>
6
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430 </repeat>
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431 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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432 <conditional name="assembly">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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433 <param name="type" value="genome"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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434 <conditional name="ref">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
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435 <param name="use_ref" value="true"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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436 <param name="r" value="reference.fna"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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437 <param name="features" value="genes.gff"/>
9
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438 <param name="operons" value="operons.bed"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
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439 <conditional name="k_mer">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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440 <param name="k_mer_stats" value="--k-mer-stats"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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441 <param name="k_mer_size" value="101" />
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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442 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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443 <param name="circos" value="true"/>
6
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444 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
445 <param name="orga_type" value=""/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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446 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
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447 <param name="min_contig" value="500"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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448 <param name="split_scaffolds" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
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449 <section name="genes">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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450 <conditional name="gene_finding">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
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451 <param name="tool" value="--gene_finding"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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452 <param name="gene_thresholds" value="0,300,1500,3000"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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453 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
454 <param name="rna_finding" value="true"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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455 <param name="conserved_genes_finding" value="true"/>
14
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parents: 13
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456 <param name="min_identity" value="95.0"/>
6
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457 </section>
9
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parents: 8
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458 <section name="alignments">
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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parents: 5
diff changeset
459 <param name="use_all_alignments" value="true"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
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460 <param name="min_alignment" value="65"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
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461 <param name="ambiguity_usage" value="one"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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462 <param name="ambiguity_score" value="0.99"/>
9
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parents: 8
diff changeset
463 </section>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
464 <section name="advanced">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
465 <param name="contig_thresholds" value="0,1000"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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diff changeset
466 <param name="strict_NA" value="true"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
467 <param name="extensive_mis_size" value="1000"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
468 <param name="scaffold_gap_max_size" value="1000"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
469 <param name="unaligned_part_size" value="500"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
470 <param name="skip_unaligned_mis_contigs" value="true"/>
6
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parents: 5
diff changeset
471 <param name="fragmented_max_indent" value="50"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
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472 </section>
9
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473 <param name="output_files" value="html"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
474 <output name="report_html" file="test1_report.html" ftype="html" compare="sim_size"/>
12
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parents: 11
diff changeset
475 <output name="circos_output" file="test1_circos.png" ftype="png" compare="sim_size"/>
0
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476 </test>
9
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parents: 8
diff changeset
477 <!-- Test 02: all outputs -->
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478 <test expect_num_outputs="8">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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479 <conditional name="in">
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diff changeset
480 <param name="custom" value="true"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
481 <repeat name="inputs">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
482 <param name="input" value="contigs1.fna"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
483 <param name="labels" value="contig1"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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484 </repeat>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
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485 <repeat name="inputs">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
486 <param name="input" value="contigs2.fna"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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diff changeset
487 <param name="labels" value="contig2"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
488 </repeat>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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489 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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diff changeset
490 <conditional name="assembly">
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parents: 8
diff changeset
491 <param name="type" value="genome"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
492 <conditional name="ref">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
493 <param name="use_ref" value="true"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
494 <param name="r" value="reference.fna"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
495 <param name="features" value="genes.gff"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
496 <param name="operons" value="operons.bed"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
497 <conditional name="k_mer">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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diff changeset
498 <param name="k_mer_stats" value="--k-mer-stats"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
499 <param name="k_mer_size" value="101" />
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
500 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
501 <param name="circos" value="true"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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parents: 8
diff changeset
502 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
503 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
504 <param name="output_files" value="html,pdf,tabular,log"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
505 <output name="report_html" file="test2_report.html" ftype="html" compare="sim_size"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
506 <output name="report_pdf" file="test2_report.pdf" ftype="pdf" compare="sim_size"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
507 <output name="report_tabular" file="test2_report.tab" ftype="tabular"/>
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
508 <output name="log" file="test2.log" ftype="txt" compare="sim_size"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
509 <output name="mis_ass" file="test2_missasemblies.tab" ftype="tabular"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
510 <output name="unalign" file="test2_unaligned.tab" ftype="tabular"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
511 <output name="kmers" file="test2_kmers.tab" ftype="tabular"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
512 <output name="circos_output" file="test2_circos.png" ftype="png" compare="sim_size"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
513 </test>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
514 <!-- Test 03: without reference -->
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
515 <test expect_num_outputs="3">
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
516 <conditional name="in">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
517 <param name="custom" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
518 <param name="inputs" value="contigs1.fna,contigs2.fna"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
519 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
520 <conditional name="assembly">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
521 <param name="type" value="genome"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
522 <conditional name="ref">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
523 <param name="use_ref" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
524 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
525 <param name="orga_type" value="--eukaryote"/>
14
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iuc
parents: 13
diff changeset
526 <param name="min_identity" value="95.0"/>
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
527 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
528 <param name="min_contig" value="500"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
529 <param name="split_scaffolds" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
530 <param name="large" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
531 <section name="genes">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
532 <conditional name="gene_finding">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
533 <param name="tool" value="none"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
534 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
535 <param name="rna_finding" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
536 <param name="conserved_genes_finding" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
537 </section>
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
538 <section name="alignments">
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
539 <param name="use_all_alignments" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
540 <param name="min_alignment" value="65"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
541 <param name="ambiguity_usage" value="one"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
542 <param name="ambiguity_score" value="0.99"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
543 <param name="fragmented" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
544 </section>
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
545 <section name="advanced">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
546 <param name="contig_thresholds" value="0,1000, 500"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
547 <param name="strict_NA" value="false"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
548 <param name="extensive_mis_size" value="1000"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
549 <param name="scaffold_gap_max_size" value="1000"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
550 <param name="unaligned_part_size" value="500"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
551 <param name="skip_unaligned_mis_contigs" value="-"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
552 </section>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
553 <param name="output_files" value="html,pdf,log" />
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
554 <output name="log" file="test3.log" ftype="txt" compare="sim_size"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
555 <output name="report_html" file="test3_report.html" compare="sim_size"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
556 <output name="report_pdf" file="test3_report.pdf" compare="sim_size"/>
3
6fcbee531de6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit cd130fcce3254cddb9a3f501f43feaa3f37c1b67
iuc
parents: 2
diff changeset
557 </test>
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
558 <!-- Test 04: metagenomics -->
14
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iuc
parents: 13
diff changeset
559 <test expect_num_outputs="3">
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
560 <conditional name="in">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
561 <param name="custom" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
562 <param name="inputs" value="contigs3.fasta"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
563 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
564 <conditional name="assembly">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
565 <param name="type" value="metagenome"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
566 <conditional name="ref">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
567 <param name="origin" value="none"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
568 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
569 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
570 <param name="min_contig" value="500"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
571 <param name="split_scaffolds" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
572 <param name="large" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
573 <section name="genes">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
574 <conditional name="gene_finding">
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
575 <param name="tool" value="--mgm"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
576 </conditional>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
577 <param name="rna_finding" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
578 <param name="conserved_genes_finding" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
579 </section>
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
580 <section name="alignments">
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
581 <param name="use_all_alignments" value="false"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
582 <param name="min_alignment" value="65"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
583 <param name="min_identity" value="95.0"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
584 <param name="ambiguity_usage" value="one"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
585 <param name="ambiguity_score" value="0.99"/>
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
586 <param name="fragmented" value="false"/>
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
587 </section>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
588 <section name="advanced">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
589 <param name="contig_thresholds" value="0,1000, 500"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
590 <param name="strict_NA" value="false"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
591 <param name="extensive_mis_size" value="1000"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
592 <param name="scaffold_gap_max_size" value="1000"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
593 <param name="unaligned_part_size" value="500"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
594 <param name="skip_unaligned_mis_contigs" value="-"/>
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
595 </section>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
596 <param name="output_files" value="log,html,tabular"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
597 <output name="log_meta" ftype="txt">
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
598 <assert_contents>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
599 <has_text text="Reference genomes are not found" />
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
600 </assert_contents>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
601 </output>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
602 <output name="report_tabular_meta" ftype="tabular">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
603 <assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
604 <has_text text="# contigs (>= 0 bp)"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
605 <has_text text="contigs3_fasta"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
606 <has_text text="# N's per 100 kbp"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
607 <has_n_lines n="17"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
608 </assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
609 </output>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
610 <output name="report_html_meta" ftype="html">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
611 <assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
612 <has_text text="Quality Assessment Tool for Genome Assemblies" />
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
613 <has_text text="contigs3_fasta" />
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
614 <has_text text="Statistics without reference" />
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
615 </assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
616 </output>
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
617 </test>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
618 <!-- Test 05: FASTQ read files -->
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
619 <test expect_num_outputs="3">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
620 <conditional name="in">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
621 <param name="custom" value="true"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
622 <repeat name="inputs">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
623 <param name="input" value="contigs1.fna"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
624 <param name="labels" value="contig1"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
625 </repeat>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
626 <repeat name="inputs">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
627 <param name="input" value="contigs2.fna"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
628 <param name="labels" value="contig2"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
629 </repeat>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
630 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
631 <conditional name="reads">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
632 <param name="reads_option" value="pacbio"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
633 <param name="input_1" value="pacbio_01.fastq,pacbio_02.fastq,pacbio_03.fastq,pacbio_04.fastq"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
634 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
635 <conditional name="assembly">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
636 <param name="type" value="genome"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
637 <conditional name="ref">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
638 <param name="use_ref" value="true"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
639 <param name="r" value="reference.fna"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
640 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
641 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
642 <section name="alignments">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
643 <param name="upper_bound_assembly" value="true"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
644 <param name="upper_bound_min_con" value="1"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
645 </section>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
646 <param name="output_files" value="tabular"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
647 <output name="report_tabular" file="test5.tab" ftype="tabular"/>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
648 <output name="mis_ass" ftype="tabular">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
649 <assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
650 <has_text text="All statistics are based on contigs of size >= 500 bp"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
651 <has_text text="# scaffold misassemblies"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
652 <has_text text="contig1"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
653 </assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
654 </output>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
655 <output name="unalign" ftype="tabular">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
656 <assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
657 <has_text text="Fully unaligned length"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
658 <has_text text="contig1"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
659 </assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
660 </output>
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
661 </test>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
662 <!-- Test 06: FASTQ.gz read files -->
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
663 <test expect_num_outputs="1">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
664 <conditional name="in">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
665 <param name="custom" value="true"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
666 <repeat name="inputs">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
667 <param name="input" value="contigs1.fna"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
668 <param name="labels" value="contig1"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
669 </repeat>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
670 <repeat name="inputs">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
671 <param name="input" value="contigs2.fna"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
672 <param name="labels" value="contig2"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
673 </repeat>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
674 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
675 <conditional name="reads">
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
676 <param name="reads_option" value="single"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
677 <param name="input_1" value="pacbio_01.fastq.gz,pacbio_02.fastq.gz"/>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
678 </conditional>
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents: 8
diff changeset
679 <param name="output_files" value="tabular"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
680 <output name="report_tabular" file="test6.tab" ftype="tabular"/>
6
f30d03867854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 911441d53ac3a7a229c448d66101bcd9179e771b
iuc
parents: 5
diff changeset
681 </test>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
682 <!-- Test 07: FASTA.gz read files -->
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 11
diff changeset
683 <test expect_num_outputs="1">
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 11
diff changeset
684 <conditional name="in">
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 11
diff changeset
685 <param name="custom" value="true"/>
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 11
diff changeset
686 <repeat name="inputs">
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 11
diff changeset
687 <param name="input" value="contigs1.fna"/>
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 11
diff changeset
688 <param name="labels" value="contig1"/>
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 11
diff changeset
689 </repeat>
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 11
diff changeset
690 <repeat name="inputs">
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 11
diff changeset
691 <param name="input" value="contigs2.fna"/>
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 11
diff changeset
692 <param name="labels" value="contig2"/>
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 11
diff changeset
693 </repeat>
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 11
diff changeset
694 </conditional>
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 11
diff changeset
695 <conditional name="reads">
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 11
diff changeset
696 <param name="reads_option" value="single"/>
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 11
diff changeset
697 <param name="input_1" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 11
diff changeset
698 </conditional>
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 11
diff changeset
699 <param name="output_files" value="tabular"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
700 <output name="report_tabular" file="test7.tab" ftype="tabular"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
701 </test>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
702 <!-- Test 08: metagenomics all tab outputs-->
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
703 <test expect_num_outputs="3">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
704 <conditional name="in">
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
705 <repeat name="inputs">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
706 <param name="input" value="meta_contigs_1.fasta"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
707 <param name="labels" value="meta_contigs_1"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
708 </repeat>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
709 <repeat name="inputs">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
710 <param name="input" value="meta_contigs_2.fasta"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
711 <param name="labels" value="meta_contigs_2"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
712 </repeat>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
713 </conditional>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
714 <conditional name="assembly">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
715 <param name="type" value="metagenome"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
716 <conditional name="ref">
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
717 <param name="origin" value="history"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
718 <param name="r" value="meta_ref_1.fasta,meta_ref_2.fasta,meta_ref_3.fasta"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
719 </conditional>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
720 <param name="min_identity" value="95.0"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
721 </conditional>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
722 <param name="min_contig" value="500"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
723 <param name="split_scaffolds" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
724 <param name="large" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
725 <section name="genes">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
726 <conditional name="gene_finding">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
727 <param name="tool" value="none"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
728 </conditional>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
729 <param name="rna_finding" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
730 <param name="conserved_genes_finding" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
731 </section>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
732 <section name="alignments">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
733 <param name="use_all_alignments" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
734 <param name="min_alignment" value="65"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
735 <param name="ambiguity_usage" value="one"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
736 <param name="ambiguity_score" value="0.99"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
737 <param name="fragmented" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
738 </section>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
739 <section name="advanced">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
740 <param name="contig_thresholds" value="0,1000"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
741 <param name="strict_NA" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
742 <param name="extensive_mis_size" value="1000"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
743 <param name="scaffold_gap_max_size" value="1000"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
744 <param name="unaligned_part_size" value="500"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
745 <param name="skip_unaligned_mis_contigs" value="-"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
746 </section>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
747 <param name="output_files" value="tabular,summary"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
748 <output name="report_tabular_meta" ftype="tabular">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
749 <assert_contents>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
750 <has_text text="# contigs (>= 0 bp)"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
751 <has_text text="meta_ref_3_fasta"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
752 <has_text text="# N's per 100 kbp"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
753 <has_n_lines n="34"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
754 </assert_contents>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
755 </output>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
756 <output_collection name="metrics_tabular" type="list" count="15"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
757 <output_collection name="metrics_pdf" type="list" count="16"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
758 </test>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
759 <!-- Test 09: metagenomics log, html and krona outputs-->
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
760 <test expect_num_outputs="2">
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
761 <conditional name="in">
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
762 <repeat name="inputs">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
763 <param name="input" value="meta_contigs_1.fasta"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
764 <param name="labels" value="meta_contigs_1"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
765 </repeat>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
766 <repeat name="inputs">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
767 <param name="input" value="meta_contigs_2.fasta"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
768 <param name="labels" value="meta_contigs_2"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
769 </repeat>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
770 </conditional>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
771 <conditional name="assembly">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
772 <param name="type" value="metagenome"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
773 <conditional name="ref">
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
774 <param name="origin" value="list"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
775 <param name="references_list" value="Lactobacillus_delbrueckii_bulgaricus,Lactobacillus_reuteri"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
776 </conditional>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
777 <param name="min_identity" value="95.0"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
778 </conditional>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
779 <param name="min_contig" value="500"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
780 <param name="split_scaffolds" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
781 <param name="large" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
782 <section name="genes">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
783 <conditional name="gene_finding">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
784 <param name="tool" value="none"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
785 </conditional>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
786 <param name="rna_finding" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
787 <param name="conserved_genes_finding" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
788 </section>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
789 <section name="alignments">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
790 <param name="use_all_alignments" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
791 <param name="min_alignment" value="65"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
792 <param name="ambiguity_usage" value="all"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
793 <param name="ambiguity_score" value="0.99"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
794 <param name="fragmented" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
795 </section>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
796 <section name="advanced">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
797 <param name="contig_thresholds" value="0,1000"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
798 <param name="strict_NA" value="false"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
799 <param name="extensive_mis_size" value="1000"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
800 <param name="scaffold_gap_max_size" value="1000"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
801 <param name="unaligned_part_size" value="500"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
802 <param name="skip_unaligned_mis_contigs" value="-"/>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
803 </section>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
804 <param name="output_files" value="html,log"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
805 <output name="report_html_meta" ftype="html">
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
806 <assert_contents>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
807 <has_text text="meta_contigs_2_fasta" />
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
808 <has_text text="combined_reference" />
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
809 <has_text text="Lactobacillus" />
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
810 </assert_contents>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
811 </output>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
812 <output name="log_meta" ftype="txt">
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
813 <assert_contents>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
814 <has_text text="List of references was provided, starting to download reference genomes from NCBI" />
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
815 <has_text text="Lactobacillus_delbrueckii_bulgaricus" />
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
816 </assert_contents>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
817 </output>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
818 </test>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
819 <!-- Test 10: Test new options -->
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
820 <test expect_num_outputs="1">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
821 <conditional name="in">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
822 <param name="custom" value="true"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
823 <repeat name="inputs">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
824 <param name="input" value="contigs1.fna"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
825 <param name="labels" value="contig1"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
826 </repeat>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
827 <repeat name="inputs">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
828 <param name="input" value="contigs2.fna"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
829 <param name="labels" value="contig2"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
830 </repeat>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
831 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
832 <section name="alignments">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
833 <param name="local_mis_size" value="210"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
834 </section>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
835 <conditional name="assembly">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
836 <param name="type" value="genome"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
837 <conditional name="ref">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
838 <param name="use_ref" value="false"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
839 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
840 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
841 <section name="advanced">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
842 <param name="report_all_metrics" value="true"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
843 <param name="x_for_Nx" value="80"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
844 </section>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
845 <param name="output_files" value="tabular"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
846 <output name="report_tabular" file="test10_tabular_report.tab" ftype="tabular"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
847 </test>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
848 <!-- Test 11: Test paired fastq.gz inputs -->
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
849 <test expect_num_outputs="1">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
850 <conditional name="in">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
851 <param name="custom" value="true"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
852 <repeat name="inputs">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
853 <param name="input" value="contigs1.fna"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
854 <param name="labels" value="contig1"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
855 </repeat>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
856 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
857 <conditional name="reads">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
858 <param name="reads_option" value="paired"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
859 <param name="input_1" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
860 <param name="input_2" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
861 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
862 <conditional name="assembly">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
863 <param name="type" value="genome"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
864 <conditional name="ref">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
865 <param name="use_ref" value="false"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
866 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
867 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
868 <param name="output_files" value="tabular"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
869 <output name="report_tabular" ftype="tabular">
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
870 <assert_contents>
14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
871 <has_text text="# contigs (>= 0 bp)"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
872 <has_text text="contig1"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
873 <has_text text="# N's per 100 kbp"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
874 <has_n_lines n="22"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
875 </assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
876 </output>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
877 </test>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
878 <!-- Test 12: Test paired-collection fastq.gz inputs -->
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
879 <test expect_num_outputs="1">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
880 <conditional name="in">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
881 <param name="custom" value="true"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
882 <repeat name="inputs">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
883 <param name="input" value="contigs1.fna"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
884 <param name="labels" value="contig1"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
885 </repeat>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
886 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
887 <conditional name="reads">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
888 <param name="reads_option" value="paired_collection"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
889 <param name="input_1">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
890 <collection type="paired">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
891 <element name="forward" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
892 <element name="reverse" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
893 </collection>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
894 </param>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
895 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
896 <conditional name="assembly">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
897 <param name="type" value="genome"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
898 <conditional name="ref">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
899 <param name="use_ref" value="false"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
900 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
901 </conditional>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
902 <param name="output_files" value="tabular"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
903 <output name="report_tabular" ftype="tabular">
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
904 <assert_contents>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
905 <has_text text="# contigs (>= 0 bp)"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
906 <has_text text="contig1"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
907 <has_text text="# N's per 100 kbp"/>
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
parents: 13
diff changeset
908 <has_n_lines n="15"/>
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
909 </assert_contents>
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
910 </output>
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 11
diff changeset
911 </test>
0
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
912 </tests>
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
913 <help>
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
914 <![CDATA[
4
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
915 **What it does**
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
916
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
917 QUAST = QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics.
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
918
8
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents: 7
diff changeset
919 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>`_.
4
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
920
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
921 **Using Quast without reference**
0
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
922
4
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
923 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:
13
675488238c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
iuc
parents: 12
diff changeset
924
4
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
925 * Quast report in HTML format
8
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents: 7
diff changeset
926 * `Contig viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents: 7
diff changeset
927 * `Quast report <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_ in Tab-delimited format
4
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
928 * Quast log (a file technical information about Quast tool execution)
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
929
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
930 The **tab delimited Quast report** will contain the following information::
0
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
931
4
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
932 Assembly pit_fna cef_fna car_fna
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
933 # contigs (>= 0 bp) 100 91 94
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
934 # contigs (>= 1000 bp) 62 58 61
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
935 Total length (>= 0 bp) 6480635 6481216 6480271
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
936 Total length (>= 1000 bp) 6466917 6468946 6467103
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
937 # contigs 71 66 70
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
938 Largest contig 848753 848766 662053
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
939 Total length 6473173 6474698 6473810
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
940 GC (%) 66.33 66.33 66.33
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
941 N50 270269 289027 254671
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
942 N75 136321 136321 146521
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
943 L50 7 7 8
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
944 L75 15 15 16
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
945 # N's per 100 kbp 0.00 0.00 0.00
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents: 3
diff changeset
946
8
ebb0dcdb621a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"
iuc
parents: 7
diff changeset
947 where values are defined as specified in `Quast manual <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_
0
736d51130b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
diff changeset
948
4
0834c823d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
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diff changeset
949 **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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950
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951 .. image:: $PATH_TO_IMAGES/contig_view_noR.png
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952 :width: 558
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953 :height: 412
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954
8
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955 Also see `Plot description <http://quast.sourceforge.net/docs/manual.html#sec2>`_ section of the manual.
4
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956
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957 **Using Quast with reference**
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958
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959 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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960
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961 * Quast report in HTML format
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962 * `Contig viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)
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963 * `Alignment viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)
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964 * `Quast report <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_ in Tab-delimited format
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965 * Summary of `misassemblies <http://quast.sourceforge.net/docs/manual.html#sec3.1.2>`_
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966 * Summary of `unaligned contigs <http://quast.sourceforge.net/docs/manual.html#sec3.1.3>`_
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967 * Quast log (a file technical information about Quast tool execution)
0
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968
4
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969 With the reference Quast produces a much more comprehensive set of results::
0
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970
4
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971 Assembly pit_fna cef_fna car_fna
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972 # contigs (>= 0 bp) 100 91 94
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973 # contigs (>= 1000 bp) 62 58 61
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974 Total length (>= 0 bp) 6480635 6481216 6480271
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975 Total length (>= 1000 bp) 6466917 6468946 6467103
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976 # contigs 71 66 70
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977 Largest contig 848753 848766 662053
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978 Total length 6473173 6474698 6473810
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979 Reference length 6537648 6537648 6537648
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980 GC (%) 66.33 66.33 66.33
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981 Reference GC (%) 66.29 66.29 66.29
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982 N50 270269 289027 254671
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983 NG50 270269 289027 254671
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984 N75 136321 136321 146521
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985 NG75 136321 136321 136321
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986 L50 7 7 8
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987 LG50 7 7 8
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988 L75 15 15 16
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989 LG75 15 15 17
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990 # misassemblies 0 0 0
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991 # misassembled contigs 0 0 0
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992 Misassembled contigs length 0 0 0
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993 # local misassemblies 1 1 2
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994 # unaligned mis. contigs 0 0 0
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995 # unaligned contigs 0 + 0 0 + 0 0 + 0
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996 part part part
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997 Unaligned length 0 0 0
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998 Genome fraction (%) 99.015 99.038 99.025
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999 Duplication ratio 1.000 1.000 1.000
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1000 # N's per 100 kbp 0.00 0.00 0.00
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1001 # mismatches per 100 kbp 3.82 3.63 3.49
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1002 # indels per 100 kbp 1.19 1.13 1.13
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1003 Largest alignment 848753 848766 662053
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1004 Total aligned length 6473163 6474660 6473792
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1005 NA50 270269 289027 254671
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1006 NGA50 270269 289027 254671
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1007 NA75 136321 136321 146521
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1008 NGA75 136321 136321 136321
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1009 LA50 7 7 8
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1010 LGA50 7 7 8
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1011 LA75 15 15 16
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1012 LGA75 15 15 17
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1013
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1014 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
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1015
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1016 Using reference also produces an **Alignment viewer**:
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1017
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1018 .. image:: $PATH_TO_IMAGES/Align_view.png
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1019 :width: 515
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1020 :height: 395
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1021
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1022 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>`_).
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1023
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1024 ]]>
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1025 </help>
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1026 <expand macro="citations"/>
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1027 </tool>