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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit cb0aff6ae5894116483d91bbb419bd4c00324cfa
author bgruening
date Wed, 18 Sep 2024 16:43:00 +0000
parents 3e4f8642c77e
children
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1 <tool id="flye" name="Flye" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01">
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2 <description>de novo assembler for single molecule sequencing reads</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="edam_ontology"/>
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7 <expand macro="xrefs"/>
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8 <expand macro="requirements" />
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9 <version_command>flye --version</version_command>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #for $counter, $input in enumerate($inputs):
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12 #if $input.is_of_type('fastqsanger', 'fastq'):
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13 #set $ext = 'fastq'
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14 #elif $input.is_of_type('fastqsanger.gz', 'fastq.gz'):
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15 #set $ext = 'fastq.gz'
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16 #elif $input.is_of_type('fasta.gz'):
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17 #set $ext = 'fasta.gz'
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18 #elif $input.is_of_type('fasta'):
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19 #set $ext = 'fasta'
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20 #end if
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21 ln -sf '$input' ./input_${counter}.${ext} &&
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22 #end for
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23 flye
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24 $mode_conditional.mode
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25 #for $counter, $input in enumerate($inputs):
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26 ./input_${counter}.$ext
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27 #end for
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28 -o out_dir
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29 -t \${GALAXY_SLOTS:-4}
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30 -i $iterations
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31 #if $mode_conditional.mode == '--pacbio-hifi' and $mode_conditional.hifi_error:
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32 --hifi-error $mode_conditional.hifi_error
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33 #end if
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34 #if $min_overlap:
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35 -m $min_overlap
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36 #end if
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37 #if $asm.asm_select == 'true':
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38 --asm-coverage $asm.asm_coverage
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39 -g '${asm.genome_size}'
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40 #end if
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41 $meta
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42 $scaffold
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43 $no_alt_contigs
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44 ]]></command>
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45 <inputs>
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46 <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="true" label="Input reads" />
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47 <conditional name="mode_conditional">
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48 <param name="mode" type="select" label="Mode">
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49 <option value="--nano-raw">Nanopore raw (--nano-raw)</option>
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50 <option value="--nano-corr">Nanopore corrected (--nano-corr)</option>
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51 <option value="--nano-hq">Nanopore HQ (--nano-hq)</option>
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52 <option value="--pacbio-raw">PacBio raw (--pacbio-raw)</option>
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53 <option value="--pacbio-corr">PacBio corrected (--pacbio-corr)</option>
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54 <option value="--pacbio-hifi">PacBio HiFi (--pacbio-hifi)</option>
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55 </param>
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56 <when value="--nano-raw"/>
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57 <when value="--nano-corr"/>
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58 <when value="--nano-hq"/>
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59 <when value="--pacbio-raw"/>
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60 <when value="--pacbio-corr"/>
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61 <when value="--pacbio-hifi">
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62 <param argument="--hifi-error" type="float" min="0" max="1" optional="true" label="Expected HiFi reads error rate" help="Default: 0.01"/>
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63 </when>
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64 </conditional>
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65 <param argument="--iterations" type="integer" value="1" label="Number of polishing iterations"
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66 help="Polishing is performed as the final assembly stage. By default, Flye runs one polishing iteration. Additional iterations
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67 might correct a small number of extra errors (due to improvements on how reads may align to the corrected assembly). If the
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68 parameter is set to 0, the polishing is not performed"/>
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69 <param argument="--min-overlap" type="integer" min="1000" max="10000" optional="true" label="Minimum overlap between reads"
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70 help="This sets a minimum overlap length for two reads to be considered overlapping. By default it is chosen
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71 automatically based on the read length distribution (reads N90) and does not require manual setting. Typical
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72 value is 3k-5k (and down to 1k for datasets with shorter read length). Intuitively, we want to set this
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73 parameter as high as possible, so the repeat graph is less tangled. However, higher values might lead to assembly gaps.
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74 In some rare cases it makes sense to manually increase minimum overlap for assemblies of big genomes with long reads and high coverage." />
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75 <param argument="--keep-haplotypes" type="boolean" truevalue="--keep-haplotypes" falsevalue="" checked="False" label="Keep haplotypes"
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76 help="By default, Flye collapses graph structures caused by alternative haplotypes (bubbles, superbubbles, roundabouts) to produce longer
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77 consensus contigs. This option retains the alternative paths on the graph, producing less contigouos, but more detailed assembly."/>
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78 <param argument="--scaffold" type="boolean" truevalue="--scaffold" falsevalue="" label="Enable scaffolding using graph"
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79 help="Starting from the version 2.9 Flye does not perform scaffolding by default, which guarantees that all assembled sequences do not have any gaps" />
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80 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="False" label="Perform metagenomic assembly"
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81 help="It is designed for highly non-uniform coverage and is sensitive to underrepresented sequence at low coverage (as low as 2x).
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82 In some examples of simple metagenomes, we observed that the normal mode assembled more contigious bacterial
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83 consensus sequence, while the metagenome mode was slightly more fragmented, but revealed strain mixtures"/>
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84 <conditional name="asm">
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85 <param name="asm_select" type="select" label="Reduced contig assembly coverage" help="Typically, assemblies of large genomes at high coverage require a hundreds of RAM. For high coverage assemblies,
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86 you can reduce memory usage by using only a subset of longest reads for initial contig extension stage (usually, the memory bottleneck)">
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87 <option value="true">Enable reduced coverage for initial disjointing assembly</option>
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88 <option value="false" selected="true">Disable reduced coverage for initial disjointing assembly</option>
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89 </param>
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90 <when value="true">
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91 <param argument="--asm-coverage" type="integer" min="0" value="30"
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92 label="Reduced coverage for initial disjointing assembly"
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93 help="This parameter specifies the target coverage of the longest reads. For a typical assembly, 30x is enough to produce good
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94 initial contigs. Regardless of this parameter, all reads will be used at the later pipeline stages."/>
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95 <param argument="--genome-size" type="text" optional="true" label="Estimated genome size"
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96 help="For example, 5m or 2.6g. No longer required as input. However, it must be used in conjunction with --asm-coverage option.">
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97 <validator type="regex" message="Genome size must be a float or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator>
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98 </param>
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99 </when>
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100 <when value="false" />
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101 </conditional>
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102 <param argument="--no-alt-contigs" type="boolean" truevalue="--no-alt-contigs" falsevalue="" checked="false" label="Remove all non-primary contigs from the assembly"/>
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103 <param name="generate_log" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate a log file"/>
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104 </inputs>
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105 <outputs>
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106 <data name="consensus" format="fasta" from_work_dir="out_dir/assembly.fasta" label="${tool.name} on ${on_string}: consensus"/>
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107 <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.gv" label="${tool.name} on ${on_string}: assembly graph"/>
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108 <data name="assembly_gfa" format="gfa" from_work_dir="out_dir/assembly_graph.gfa" label="${tool.name} on ${on_string}: graphical fragment assembly"/>
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109 <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string}: assembly info"/>
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110 <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${tool.name} on ${on_string}: log">
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111 <filter>generate_log</filter>
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112 </data>
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113 </outputs>
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114 <tests>
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115 <!--Test 01: pacbio-raw-->
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116 <test expect_num_outputs="5">
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117 <param name="inputs" ftype="fastq.gz" value="ecoli_01.fastq.gz,ecoli_02.fastq.gz,ecoli_03.fastq.gz,ecoli_04.fastq.gz,ecoli_05.fastq.gz,ecoli_06.fastq.gz,ecoli_07.fastq.gz"/>
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118 <param name="mode" value="--pacbio-raw"/>
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119 <param name="iterations" value="0"/>
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120 <param name="generate_log" value="true"/>
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121 <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular" compare="sim_size"/>
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122 <output name="assembly_graph" file="result1_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
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123 <output name="assembly_gfa" file="result1_assembly_graph.gfa" ftype="gfa" compare="diff" lines_diff="10"/>
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124 <output name="consensus" ftype="fasta">
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125 <assert_contents>
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126 <has_line line=">contig_1"/>
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127 </assert_contents>
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128 </output>
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129 <output name="flye_log" file="result1.log" ftype="txt" compare="sim_size"/>
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130 </test>
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131 <!--Test 02: nano raw-->
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132 <test expect_num_outputs="4">
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133 <param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/>
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134 <param name="mode" value="--nano-raw"/>
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135 <param name="iterations" value="0"/>
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136 <output name="assembly_info" ftype="tabular">
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137 <assert_contents>
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138 <has_size value="95" delta="100"/>
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139 </assert_contents>
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140 </output>
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141 <output name="assembly_graph" ftype="graph_dot">
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142 <assert_contents>
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143 <has_size value="803" delta="100"/>
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144 </assert_contents>
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145 </output>
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146 <output name="assembly_gfa" ftype="gfa">
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147 <assert_contents>
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148 <has_size value="35047" delta="100"/>
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149 </assert_contents>
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150 </output>
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151 <output name="consensus" ftype="fasta">
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152 <assert_contents>
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153 <has_size value="35573" delta="100"/>
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154 </assert_contents>
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155 </output>
4
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156 </test>
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157 <!--Test 03: reduce coverage-->
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158 <test expect_num_outputs="4">
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159 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/>
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160 <conditional name="mode_conditional">
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161 <param name="mode" value="--nano-raw"/>
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162 </conditional>
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163 <conditional name="asm">
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parents: 5
diff changeset
164 <param name="asm_select" value="true" />
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
165 <param name="asm" value="30"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
166 <param name="genome_size" value="3980000"/>
6
0284be52bfcf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents: 5
diff changeset
167 </conditional>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
168 <output name="assembly_info" ftype="tabular">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
169 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
170 <has_size value="286" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
171 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
172 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
173 <output name="assembly_graph" ftype="graph_dot">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
174 <assert_contents>
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
175 <has_size value="1840" delta="100"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
176 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
177 </output>
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 11
diff changeset
178 <output name="assembly_gfa" ftype="gfa">
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
179 <assert_contents>
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
180 <has_size value="420752" delta="100"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
181 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
182 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
183 <output name="consensus" ftype="fasta">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
184 <assert_contents>
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
185 <has_size value="427580" delta="100"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
186 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
187 </output>
0
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
188 </test>
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
189 <!--Test 04: metagenomic mode-->
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
190 <test expect_num_outputs="4">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
191 <param name="inputs" ftype="fastq.gz" value="ecoli_01.fastq.gz,ecoli_02.fastq.gz,ecoli_03.fastq.gz,ecoli_04.fastq.gz,ecoli_05.fastq.gz,ecoli_06.fastq.gz,ecoli_07.fastq.gz"/>
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
192 <conditional name="mode_conditional">
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
193 <param name="mode" value="--pacbio-raw"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
194 </conditional>
4
3ee0ef312022 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 1143ac8397d6fefb3f18d33bb752ee3f13c072d6"
bgruening
parents: 3
diff changeset
195 <param name="meta" value="true"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
196 <output name="assembly_info" ftype="tabular">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
197 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
198 <has_size value="95" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
199 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
200 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
201 <output name="assembly_graph" ftype="graph_dot">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
202 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
203 <has_size value="367" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
204 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
205 </output>
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 11
diff changeset
206 <output name="assembly_gfa" ftype="gfa">
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
207 <assert_contents>
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
208 <has_size value="418729" delta="100"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
209 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
210 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
211 <output name="consensus" ftype="fasta">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
212 <assert_contents>
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
213 <has_size value="425667" delta="100"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
214 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
215 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
216 </test>
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
217 <!--Test 05: nanopore HQ mode-->
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
218 <test expect_num_outputs="4">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
219 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/>
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
220 <conditional name="mode_conditional">
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
221 <param name="mode" value="--nano-hq"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
222 </conditional>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
223 <param name="min_overlap" value="1000"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
224 <output name="assembly_info" ftype="tabular">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
225 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
226 <has_size value="286" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
227 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
228 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
229 <output name="assembly_graph" ftype="graph_dot">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
230 <assert_contents>
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
231 <has_size value="1248" delta="100"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
232 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
233 </output>
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 11
diff changeset
234 <output name="assembly_gfa" ftype="gfa">
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
235 <assert_contents>
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 11
diff changeset
236 <has_size value="419414" delta="1000"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
237 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
238 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
239 <output name="consensus" ftype="fasta">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
240 <assert_contents>
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 11
diff changeset
241 <has_size value="426277" delta="1000"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
242 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
243 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
244 </test>
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
245 <!--Test 06: hifi error option-->
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
246 <test expect_num_outputs="4">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
247 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/>
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
248 <conditional name="mode_conditional">
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
249 <param name="mode" value="--pacbio-hifi"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
250 <param name="hifi_error" value="0.21"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
251 </conditional>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
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diff changeset
252 <param name="min_overlap" value="1000"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
253 <output name="assembly_info" ftype="tabular">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
254 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
255 <has_size value="286" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
256 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
257 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
258 <output name="assembly_graph" ftype="graph_dot">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
259 <assert_contents>
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 11
diff changeset
260 <has_size value="1248" delta="500"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
261 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
262 </output>
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 11
diff changeset
263 <output name="assembly_gfa" ftype="gfa">
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
264 <assert_contents>
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 11
diff changeset
265 <has_size value="420254" delta="2000"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
266 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
267 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
268 <output name="consensus" ftype="fasta">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
269 <assert_contents>
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 11
diff changeset
270 <has_size value="427131" delta="2000"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
271 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
272 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
273 </test>
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
274 <!--Test 07: keep haplotypes-->
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
275 <test expect_num_outputs="4">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
276 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/>
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
277 <conditional name="mode_conditional">
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
278 <param name="mode" value="--pacbio-corr"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
279 <param name="hifi_error" value="0.21"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
280 </conditional>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
281 <param name="min_overlap" value="1000"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
282 <param name="keep-haplotypes" value="true"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
283 <output name="assembly_info" ftype="tabular">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
284 <assert_contents>
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 11
diff changeset
285 <has_size value="286" delta="200"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
286 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
287 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
288 <output name="assembly_graph" ftype="graph_dot">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
289 <assert_contents>
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 11
diff changeset
290 <has_size value="1273" delta="500"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
291 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
292 </output>
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 11
diff changeset
293 <output name="assembly_gfa" ftype="gfa">
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
294 <assert_contents>
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 11
diff changeset
295 <has_size value="420254" delta="3000"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
296 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
297 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
298 <output name="consensus" ftype="fasta">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
299 <assert_contents>
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 11
diff changeset
300 <has_size value="427131" delta="3000"/>
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
301 </assert_contents>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
302 </output>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
303 </test>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
304 <!--Test 08: scaffolding mode-->
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
305 <test expect_num_outputs="4">
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
306 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
307 <param name="mode" value="--nano-hq"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
308 <param name="min_overlap" value="1000"/>
11
291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e
bgruening
parents: 10
diff changeset
309 <param name="scaffold" value="true"/>
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
310 <output name="assembly_info" ftype="tabular">
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
311 <assert_contents>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
312 <has_size value="286" delta="100"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
313 </assert_contents>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
314 </output>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
315 <output name="assembly_graph" ftype="graph_dot">
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
316 <assert_contents>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
317 <has_size value="1248" delta="100"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
318 </assert_contents>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
319 </output>
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 11
diff changeset
320 <output name="assembly_gfa" ftype="gfa">
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
321 <assert_contents>
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 11
diff changeset
322 <has_size value="419414" delta="2000"/>
9
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
323 </assert_contents>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
324 </output>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
325 <output name="consensus" ftype="fasta">
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 8
diff changeset
326 <assert_contents>
12
3e4f8642c77e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 11
diff changeset
327 <has_size value="426277" delta="2000"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
328 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
329 </output>
0
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
330 </test>
10
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 9
diff changeset
331 <!--Test 09: test not-alt-contigs parameter w-->
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 9
diff changeset
332 <test expect_num_outputs="4">
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 9
diff changeset
333 <param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 9
diff changeset
334 <param name="mode" value="--nano-raw"/>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 9
diff changeset
335 <param name="iterations" value="0"/>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 9
diff changeset
336 <param name="no_alt_contigs" value="true"/>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 9
diff changeset
337 <output name="assembly_info" ftype="tabular">
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
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338 <assert_contents>
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339 <has_size value="151" delta="100"/>
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340 </assert_contents>
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341 </output>
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342 <output name="assembly_graph" ftype="graph_dot">
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343 <assert_contents>
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344 <has_size value="217" delta="100"/>
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345 </assert_contents>
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346 </output>
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347 <output name="assembly_gfa" ftype="gfa">
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348 <assert_contents>
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349 <has_size value="5110" delta="100"/>
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350 </assert_contents>
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351 </output>
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352 <output name="consensus" ftype="fasta">
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353 <assert_contents>
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354 <has_size value="5123" delta="100"/>
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355 </assert_contents>
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356 </output>
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357 </test>
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358 </tests>
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359 <help><![CDATA[
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360
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361 **Purpose**
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362
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363 Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies.
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364 It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents
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365 a complete pipeline: it takes raw PacBio/ONT reads as input and outputs polished contigs. Flye also has a special mode for metagenome
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366 assembly.
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367
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368 ----
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369
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370 **Quick usage**
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371
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372 Input reads can be in FASTA or FASTQ format, uncompressed or compressed with gz. Currently, PacBio (raw, corrected, HiFi) and ONT reads
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373 (raw, corrected) are supported. Expected error rates are <30% for raw, <3% for corrected, and <1% for HiFi. Note that Flye was primarily
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374 developed to run on raw reads. You may specify multiple files with reads (separated by spaces). Mixing different read types is not yet supported. The *--meta* o
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375 ption enables the mode for metagenome/uneven coverage assembly.
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376
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377 Genome size estimate is no longer a required option. You need to provide an estimate if using *--asm-coverage* option.
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378
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379 To reduce memory consumption for large genome assemblies, you can use a subset of the longest reads for initial disjointig assembly by
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380 specifying *--asm-coverage* and *--genome-size* options. Typically, 40x coverage is enough to produce good disjointigs.
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381
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382 ----
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383
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384 **Outputs**
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385
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386 The main output files are:
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387
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388 * Final assembly: contains contigs and possibly scaffolds (see below).
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389 * Final repeat graph: note that the edge sequences might be different (shorter) than contig sequences, because contigs might include multiple graph edges.
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390 * Extra information about contigs (such as length or coverage).
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391
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392 Each contig is formed by a single unique graph edge. If possible, unique contigs are extended with the sequence from flanking unresolved repeats on the graph. Thus,
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393 a contig fully contains the corresponding graph edge (with the same id), but might be longer then this edge. This is somewhat similar to unitig-contig relation in
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394 OLC assemblers. In a rare case when a repetitive graph edge is not covered by the set of "extended" contigs, it will be also output in the assembly file.
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395
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396 Sometimes it is possible to further order contigs into scaffolds based on the repeat graph structure. These ordered contigs will be output as a part of scaffold in
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397 the assembly file (with a scaffold prefix). Since it is hard to give a reliable estimate of the gap size, those gaps are represented with the default 100 Ns.
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398 assembly_info.txt file (below) contains additional information about how scaffolds were formed.
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399
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400 Extra information about contigs/scaffolds is output into the assembly_info.txt file. It is a tab-delimited table with the columns as follows:
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401
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402 * Contig/scaffold id
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403 * Length
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404 * Coverage
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405 * Is circular, (Y)es or (N)o
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406 * Is repetitive, (Y)es or (N)o
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407 * Multiplicity (based on coverage)
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408 * Alternative group
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409 * Graph path (graph path corresponding to this contig/scaffold).
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410
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411 Scaffold gaps are marked with `??` symbols, and `*` symbol denotes a terminal graph node. Alternative contigs (representing alternative haplotypes) will have the same alt.
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412 group ID. Primary contigs are marked by `*`.
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413
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414 ----
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415
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416 **Algorithm Description**
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417
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418 This is a brief description of the Flye algorithm. Please refer to the manuscript for more detailed information. The draft contig extension is organized as follows:
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419
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420 * K-mer counting / erroneous k-mer pre-filtering
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421 * Solid k-mer selection (k-mers with sufficient frequency, which are unlikely to be erroneous)
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422 * Contig extension. The algorithm starts from a single read and extends it with a next overlapping read (overlaps are dynamically detected using the selected solid k-mers).
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423
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424 Note that we do not attempt to resolve repeats at this stage, thus the reconstructed contigs might contain misassemblies. Flye then aligns the reads on these draft
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425 contigs using minimap2 and calls a consensus. Afterwards, Flye performs repeat analysis as follows:
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426
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427 * Repeat graph is constructed from the (possibly misassembled) contigs
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428 * In this graph all repeats longer than minimum overlap are collapsed
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429 * The algorithm resolves repeats using the read information and graph structure
291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e
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430 * The unbranching paths in the graph are output as contigs
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431
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432 If enabled, after resolving bridged repeats, Trestle module attempts to resolve simple unbridged repeats (of multiplicity 2) using the heterogeneities between repeat copies.
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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433 Finally, Flye performs polishing of the resulting assembly to correct the remaining errors:
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
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434
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435 * Alignment of all reads to the current assembly using minimap2
291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e
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436 * Partition the alignment into mini-alignments (bubbles)
291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e
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437 * Error correction of each bubble using a maximum likelihood approach
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438
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439 The polishing steps could be repeated, which might slightly increase quality for some datasets.
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440
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441
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442 ]]></help>
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443 <expand macro="citations" />
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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444 </tool>