annotate unicycler.xml @ 12:3e44ef016b45 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit bc948510a50635ce98123c9e09ae09b39f1e5cee
author iuc
date Sun, 07 Jul 2024 19:46:39 +0000
parents 8f9f06995f98
children e022dff952df
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1 <tool id="unicycler" name="Create assemblies with Unicycler" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
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2 <description>pipeline for bacterial genomes</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.5.0</token>
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5 <token name="@VERSION_SUFFIX@">2</token>
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6 </macros>
7
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
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7 <edam_topics>
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
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8 <edam_topic>topic_0196</edam_topic>
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
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9 </edam_topics>
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
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10 <edam_operations>
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
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11 <edam_operation>operation_0525</edam_operation>
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
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12 </edam_operations>
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13 <xrefs>
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14 <xref type="bio.tools">unicycler</xref>
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15 </xrefs>
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16 <requirements>
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17 <requirement type="package" version="@TOOL_VERSION@">unicycler</requirement>
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18 <requirement type="package" version="1.15.1">samtools</requirement>
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19 </requirements>
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20 <command detect_errors="exit_code"><![CDATA[
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21 #for r in $reuse
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22 ln -s $r.reuse_file ${r.reuse_step}.gfa &&
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23 #end for
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24
2
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25 ## Preparing files
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26 #if str( $paired_unpaired.fastq_input_selector ) == "paired"
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27 #if $paired_unpaired.fastq_input1.is_of_type("fastq.gz"):
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28 #set fq1 = "fq1.fastq.gz"
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29 #else
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30 #set fq1 = "fq1.fastq"
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31 #end if
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32 #if $paired_unpaired.fastq_input2.is_of_type("fastq.gz"):
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33 #set fq2 = "fq2.fastq.gz"
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34 #else
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35 #set fq2 = "fq2.fastq"
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36 #end if
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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37 ln -s '${paired_unpaired.fastq_input1}' $fq1 &&
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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38 ln -s '${paired_unpaired.fastq_input2}' $fq2 &&
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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39 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection"
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40 #if $paired_unpaired.fastq_input1.forward.is_of_type("fastq.gz"):
3e44ef016b45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit bc948510a50635ce98123c9e09ae09b39f1e5cee
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41 #set fq1 = "fq1.fastq.gz"
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42 #else
2
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43 #set fq1 = "fq1.fastq"
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44 #end if
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45 #if $paired_unpaired.fastq_input1.reverse.is_of_type("fastq.gz"):
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46 #set fq2 = "fq2.fastq.gz"
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47 #else
2
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48 #set fq2 = "fq2.fastq"
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49 #end if
2
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50 ln -s '${paired_unpaired.fastq_input1.forward}' $fq1 &&
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51 ln -s '${paired_unpaired.fastq_input1.reverse}' $fq2 &&
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52 #elif str( $paired_unpaired.fastq_input_selector ) == "single"
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53 #if $paired_unpaired.fastq_input1.is_of_type("fastqsanger.gz"):
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54 #set fq = "fq.fastq.gz"
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55 #else
2
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56 #set fq = "fq.fastq"
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57 #end if
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58 ln -s '${paired_unpaired.fastq_input1}' '$fq' &&
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59 #end if
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60 #if $long
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61 #if $long.is_of_type("fastq"):
2
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62 #set lr = "lr.fastq"
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63 #elif $long.is_of_type("fastq.gz"):
2
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64 #set lr = "lr.fastq.gz"
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65 #elif $long.is_of_type("fasta")
2
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66 #set lr = "lr.fasta"
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67 #end if
2
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68 ln -s '${long}' '$lr' &&
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69 #end if
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70 ## Running Unicycler
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71 unicycler -t "\${GALAXY_SLOTS:-4}"
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72 -o ./
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73 --verbosity 3
4
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74 #if str( $paired_unpaired.fastq_input_selector ) == "paired"
2
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75 -1 '$fq1'
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76 -2 '$fq2'
4
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77 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection"
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78 -1 '$fq1'
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79 -2 '$fq2'
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80 #elif str( $paired_unpaired.fastq_input_selector ) == "single"
2
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81 -s '$fq'
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82 #end if
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83 #if $long
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84 -l $lr
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85 #end if
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86 ## General Unicycler Options section
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87 ## ----------------------------------------------------------
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88 --mode '$mode'
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89 --min_fasta_length '$min_fasta_length'
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90 --linear_seqs '$linear_seqs'
4
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91 #if str($min_anchor_seg_len) != ''
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92 --min_anchor_seg_len '$min_anchor_seg_len'
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93 #end if
2
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94 ## Spades Options section
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95 ## ----------------------------------------------------------
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96 --min_kmer_frac '$spades.min_kmer_frac'
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97 --max_kmer_frac '$spades.max_kmer_frac'
4
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98 #if str($spades.kmers) != ''
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99 --kmers '$spades.kmers'
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100 #end if
2
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101 --kmer_count '$spades.kmer_count'
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102 --depth_filter '$spades.depth_filter'
7
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
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103 #if $spades.largest_component
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
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104 --largest_component
88c240872a65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
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105 #end if
2
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106 ## Rotation Options section
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107 ## ----------------------------------------------------------
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108 $rotation.no_rotate
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109 #if $rotation.start_genes
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110 --start_genes '$rotation.start_genes'
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111 #end if
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112 --start_gene_id '$rotation.start_gene_id'
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113 --start_gene_cov '$rotation.start_gene_cov'
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114 ## Graph cleaning Options sdection
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115 ## ----------------------------------------------------------
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116 --min_component_size '$graph_clean.min_component_size'
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117 --min_dead_end_size '$graph_clean.min_dead_end_size'
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118 ## Long Read Alignment Options
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119 ## ----------------------------------------------------------
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120 #if $lr_align.contamination
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121 --contamination '$lr_align.contamination'
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122 #end if
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123 --scores '${lr_align.scores}'
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124 #if str($lr_align.low_score) != ''
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125 --low_score '$lr_align.low_score'
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126 #end if
9
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127 $lr_align.no_simple_bridges
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128 --keep $keep
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129 #if $keep != '0'
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130 && mkdir 'spades_graphs'
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131 && mv 00*gfa './spades_graphs/'
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132 #end if
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133 #if $keep == '2' and $long
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134 && samtools view -@ "\${GALAXY_SLOTS:-4}" -u 'read_alignment/long_read_alignments.sam' | samtools sort -@ "\${GALAXY_SLOTS:-4}" -o 'read_alignment/long_read_alignments.bam'
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135 #end if
0
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136 ]]></command>
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137 <inputs>
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138 <conditional name="paired_unpaired">
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139 <param name="fastq_input_selector" type="select" label="Paired or Single end data?" help="Select between paired and single end data">
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140 <option selected="True" value="paired">Paired</option>
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141 <option value="paired_collection">Paired Collection</option>
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142 <option value="single">Single</option>
4
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143 <option value="none">None</option>
0
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144 </param>
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145 <when value="paired">
10
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146 <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz"
6
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147 label="Select first set of reads" help="Specify dataset with forward reads"/>
10
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148 <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz"
6
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149 label="Select second set of reads" help="Specify dataset with reverse reads"/>
0
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150 </when>
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151 <when value="paired_collection">
10
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152 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" type="data_collection" collection_type="paired" label="Select a paired collection" />
0
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153 </when>
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154 <when value="single">
10
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155 <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz"
6
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156 label="Select unpaired reads" help="Specify dataset with unpaired reads"/>
0
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157 </when>
4
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158 <when value="none">
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159 </when>
0
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160 </conditional>
10
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161 <param argument="--long" optional="true" type="data" format="fastqsanger,fastqsanger.gz,fasta,fastq,fastq.gz" label="Select long reads. If there are no long reads, leave this empty"/>
2
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162 <param argument="--mode" type="select" label="Select Bridging mode">
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163 <option value="conservative">Conservative (smaller contigs, lower misassembly)</option>
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164 <option value="normal" selected="True">Normal (moderate contig size and misassembly rate)</option>
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165 <option value="bold">Bold (longest contigs, higher misassembly rate)</option>
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166 </param>
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167 <param argument="--min_fasta_length" type="integer" value="100" label="Exclude contigs from the FASTA file which are shorter than this length (bp)"/>
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168 <param argument="--linear_seqs" type="integer" value="0" label="The expected number of linear (i.e. non-circular) sequences in the assembly"/>
4
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169 <param argument="--min_anchor_seg_len" type="integer" min="0" optional="true" label="Unicycler will not use segments shorter than this as scaffolding anchors"/>
6
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170 <section name="spades" expanded="False" title="SPAdes options"
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171 help="Unicycler uses SPAdes to construct assembly graphs. You can modify some of the SPAdes settings here. Use this ONLY if you know what you are doing!">
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172 <param argument="--min_kmer_frac" type="float" min="0" max="1" value="0.2"
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173 label="Lowest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/>
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174 <param argument="--max_kmer_frac" type="float" min="0" max="1" value="0.95"
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175 label="Highest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/>
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176 <param argument="--kmers" type="text" value="" optional="true" label="Exact k-mers to use for SPAdes assembly, comma-separated">
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177 <validator type="regex" message="Kmers must be comma-separated odd integers (no repitition) without space in the range of 11 to 127 (inclusive)">^(\d*[13579],)*(\d*[13579])$</validator>
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178 </param>
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179 <param argument="--kmer_count" type="integer" min="0" value="10" label="Number of k-mer steps to use in SPAdes assembly"/>
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180 <param argument="--depth_filter" type="float" min="0" max="1" value="0.25"
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181 label="Filter out contigs lower than this fraction of the chromosomal depth" help="It is done if does not result in graph dead ends"/>
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182 <param argument="--largest_component" type="boolean" checked="false"
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183 label="Only keep the largest connected component of the assembly graph"/>
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184 </section>
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185 <section name="rotation" expanded="false" title="Rotation options"
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186 help="These options control the rotation of completed circular sequence near the end of the Unicycler pipeline. Use this ONLY if you know what you are doing!">
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187 <param argument="--no_rotate" type="boolean" checked="false" truevalue="--no_rotate" falsevalue=""
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188 label="Do not rotate completed replicons to start at a standard gene." help="Unicycler uses TBLASTN to search for dnaA or repA alleles in each completed replicon. If one is found, the sequence is rotated and/or flipped so that it begins with that gene encoded on the forward strand. This provides consistently oriented assemblies and reduces the risk that a gene will be split across the start and end of the sequence."/>
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189 <param argument="--start_genes" optional="true" type="data" format="fasta" label="FASTA file of genes for start point of rotated replicons" />
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190 <param argument="--start_gene_id" type="float" min="0" max="100" value="90" label="The minimum required BLAST percent identity for a start gene search"/>
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191 <param argument="--start_gene_cov" type="float" min="0" max="100" value="95" label="The minimum required BLAST percent coverage for a start gene search"/>
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192 </section>
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193 <section name="graph_clean" expanded="false" title="Graph cleaning options"
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194 help="These options control the removal of small leftover sequences after bridging is complete.">
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195 <param argument="--min_component_size" type="integer" min="0" value="1000"
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196 label="Unbridged graph components smaller than this size will be removed from the final graph" />
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197 <param argument="--min_dead_end_size" type="integer" min="0" value="1000"
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198 label="Graph dead ends smaller than this size will be removed from the final graph"/>
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199 </section>
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200 <section name="lr_align" expanded="false" title="Long read alignment parameters" help="These options control the alignment of long reads to the assembly graph.">
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201 <param argument="--contamination" optional="true" type="data" format="fasta"
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202 label="FASTA file of known contamination in long reads, e.g. lambda, phiXm or puc18 spike-ins." />
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203 <param argument="--scores" type="text" value="3,-6,-5,-2" label="Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend"/>
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204 <param argument="--low_score" optional="true" type="integer" value=""
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205 label="Score threshold - alignments below this are considered poor" help="default = set automatically"/>
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206 <param argument="--no_simple_bridges" type="boolean" truevalue="--no_simple_bridges" falsevalue="" checked="false" label="Simple long-read bridging" help="Default: No" />
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207 </section>
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208 <param argument="--keep" type="select" label="Outputs to keep" help="Level of file retention. Default: 1">
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209 <option value="0">0: only keep final files</option>
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210 <option value="1" selected="true">1: save graphs at main checkpoints</option>
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211 <option value="2">2: also keep SAM</option>
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212 </param>
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213 <repeat name="reuse" title="Reuse checkpoint files from earlier runs" max="1" help="">
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214 <param name="reuse_file" type="data" optional="false" format="gfa1" label="Checkpoint file"/>
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215 <param name="reuse_step" type="select" label="Checkpoint">
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216 <option value="002_depth_filter">002_depth_filter</option>
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217 <option value="003_overlaps_removed">003_overlaps_removed</option>
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218 <option value="004_bridges_applied">004_bridges_applied</option>
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219 </param>
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220 </repeat>
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221 </inputs>
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222 <outputs>
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223 <data name="assembly_graph" format="gfa1" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" />
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224 <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/>
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225 <collection name="spades_collection" type="list" label="${tool.name} on ${on_string}: SPAdes graphs">
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226 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.gfa" format="gfa1" directory="spades_graphs"/>
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227 <filter>keep != "0"</filter>
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228 </collection>
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229 <data name="bam_file" format="bam" from_work_dir="read_alignment/long_read_alignments.bam" label="${tool.name} on ${on_string}: Long read alignments BAM">
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230 <filter>keep == "2" and long</filter>
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231 </data>
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232 </outputs>
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233 <tests>
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234 <test expect_num_outputs="2">
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235 <conditional name="paired_unpaired">
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236 <param name="fastq_input_selector" value="paired" />
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237 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" />
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238 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" />
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239 </conditional>
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240 <param name="mode" value="normal" />
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241 <param name="min_fasta_length" value="100"/>
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242 <param name="linear_seqs" value="0"/>
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243 <section name="spades">
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244 <param name="min_kmer_frac" value="0.2"/>
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245 <param name="max_kmer_frac" value="0.95"/>
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246 <param name="kmer_count" value="10"/>
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247 <param name="depth_filter" value="0.25"/>
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248 </section>
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249 <section name="rotation">
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250 <param name="no_rotate" value=""/>
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251 <param name="start_gene_id" value="90"/>
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252 <param name="start_gene_cov" value="95"/>
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253 </section>
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254 <section name="graph_clean">
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255 <param name="min_component_size" value="1000"/>
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256 <param name="min_dead_end_size" value="1000"/>
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257 </section>
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258 <section name="lr_align">
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259 <param name="scores" value="3,-6,-5,-2"/>
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260 </section>
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261 <param name="keep" value="0"/>
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262 <output name="assembly_graph" ftype="gfa1">
2
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263 <assert_contents>
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264 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/>
2
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265 </assert_contents>
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266 </output>
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267 <output name="assembly" ftype="fasta">
0
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268 <assert_contents>
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269 <has_text text="length=5386" />
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270 </assert_contents>
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271 </output>
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272 </test>
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273 <!--
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274 Following test corresponds to the command:
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275
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276 unicycler -t "${GALAXY_SLOTS:-8}" -o ./ - -verbose 3 - -pilon_path `pilon - -jar_dir` \
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277 -1 test-data/phix_f.fq.gz -2 test-data/phix_r.fq.gz -l test-data/onp.fa \
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278 - -mode 'normal' - -no_correct
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279
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280 This command causes a segfault with the current version of unicycler on bioconda for Linux
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281 during the minimap step (which seems to be compiled C code). A gist of the log can be found
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282 at: https://gist.github.com/jmchilton/b411b695170c1daea6589f5d76e326cb.
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283 -->
9
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284 <test expect_num_outputs="2">
2
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285 <conditional name="paired_unpaired">
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286 <param name="fastq_input_selector" value="paired" />
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287 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger.gz" />
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288 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger.gz" />
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289 </conditional>
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290 <param name="long" value="onp.fa" ftype="fasta" />
0
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291 <param name="mode" value="normal" />
2
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292 <param name="min_fasta_length" value="100"/>
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293 <param name="linear_seqs" value="0"/>
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294 <section name="spades">
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295 <param name="min_kmer_frac" value="0.2"/>
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296 <param name="max_kmer_frac" value="0.95"/>
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297 <param name="kmer_count" value="10"/>
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298 <param name="depth_filter" value="0.25"/>
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299 </section>
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300 <section name="rotation">
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301 <param name="no_rotate" value=""/>
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302 <param name="start_gene_id" value="90"/>
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303 <param name="start_gene_cov" value="95"/>
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304 </section>
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305 <section name="graph_clean">
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306 <param name="min_component_size" value="1000"/>
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307 <param name="min_dead_end_size" value="1000"/>
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308 </section>
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309 <section name="lr_align">
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310 <param name="scores" value="3,-6,-5,-2"/>
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311 </section>
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312 <param name="keep" value="0"/>
8
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313 <output name="assembly_graph" ftype="gfa1">
2
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314 <assert_contents>
8
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315 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/>
2
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316 </assert_contents>
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317 </output>
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318 <output name="assembly" ftype="fasta">
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319 <assert_contents>
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320 <has_text text="length=5386" />
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321 </assert_contents>
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322 </output>
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323 </test>
9
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324 <test expect_num_outputs="2">
2
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325 <conditional name="paired_unpaired">
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326 <param name="fastq_input_selector" value="paired_collection"/>
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327 <param name="fastq_input1">
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328 <collection type="paired">
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329 <element name="forward" value="phix_f.fq.gz" ftype="fastqsanger" />
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330 <element name="reverse" value="phix_r.fq.gz" ftype="fastqsanger" />
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331 </collection>
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332 </param>
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333 </conditional>
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334 <param name="mode" value="normal" />
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335 <param name="min_fasta_length" value="100"/>
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336 <param name="linear_seqs" value="0"/>
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337 <section name="spades">
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338 <param name="min_kmer_frac" value="0.2"/>
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339 <param name="max_kmer_frac" value="0.95"/>
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340 <param name="kmer_count" value="10"/>
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341 <param name="depth_filter" value="0.25"/>
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342 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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343 <section name="rotation">
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iuc
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344 <param name="no_rotate" value=""/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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345 <param name="start_gene_id" value="90"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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346 <param name="start_gene_cov" value="95"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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347 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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348 <section name="graph_clean">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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349 <param name="min_component_size" value="1000"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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350 <param name="min_dead_end_size" value="1000"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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351 </section>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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352 <section name="lr_align">
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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353 <param name="scores" value="3,-6,-5,-2"/>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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354 </section>
9
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355 <param name="keep" value="0"/>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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356 <output name="assembly_graph" ftype="gfa1">
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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357 <assert_contents>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
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358 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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359 </assert_contents>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
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360 </output>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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361 <output name="assembly" ftype="fasta">
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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362 <assert_contents>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
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363 <has_text text="length=5386" />
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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364 </assert_contents>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
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365 </output>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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366 </test>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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367 <test expect_num_outputs="2">
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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368 <conditional name="paired_unpaired">
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
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369 <param name="fastq_input_selector" value="none"/>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
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370 </conditional>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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371 <param name="min_anchor_seg_len" value="10"/>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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372 <section name="spades">
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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373 <param name="kmers" value="21,23"/>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
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374 </section>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
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375 <param name="long" value="only_long.fasta" ftype="fasta" />
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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376 <param name="keep" value="0"/>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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377 <output name="assembly_graph" ftype="gfa1">
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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378 <assert_contents>
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iuc
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379 <has_text text="S" />
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
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380 </assert_contents>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
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381 </output>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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382 <output name="assembly" ftype="fasta">
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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383 <assert_contents>
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iuc
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384 <has_text text=">1" />
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
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385 </assert_contents>
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386 </output>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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387 </test>
11
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388 <!-- test checkpoint graph reuse
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
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389 TODO more precise test and check difference to call wo reuse -->
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
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390 <test expect_num_outputs="2">
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
391 <conditional name="paired_unpaired">
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
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392 <param name="fastq_input_selector" value="paired_collection"/>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
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393 <param name="fastq_input1">
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
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394 <collection type="paired">
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iuc
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diff changeset
395 <element name="forward" value="phix_f.fq.gz" ftype="fastqsanger" />
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
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396 <element name="reverse" value="phix_r.fq.gz" ftype="fastqsanger" />
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
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397 </collection>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
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398 </param>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
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399 </conditional>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
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400 <param name="long" value="only_long.fasta" ftype="fasta" />
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
401 <repeat name="reuse">
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
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402 <param name="reuse_file" value="phix__spades_graph.gfa1"/>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
403 <param name="reuse_step" value="002_depth_filter"/>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
404 </repeat>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
405 <param name="keep" value="0"/>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
406 <output name="assembly_graph" ftype="gfa1">
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
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407 <assert_contents>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
408 <has_text text="S" />
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
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409 </assert_contents>
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410 </output>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
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411 <output name="assembly" ftype="fasta">
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
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412 <assert_contents>
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iuc
parents: 10
diff changeset
413 <has_text text=">1" />
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
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414 </assert_contents>
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415 </output>
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iuc
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diff changeset
416 </test>
9
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417 <!-- Test keep value = 1 -->
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iuc
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418 <test expect_num_outputs="3">
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
419 <conditional name="paired_unpaired">
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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diff changeset
420 <param name="fastq_input_selector" value="paired" />
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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diff changeset
421 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" />
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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diff changeset
422 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" />
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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423 </conditional>
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iuc
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diff changeset
424 <param name="mode" value="normal" />
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
425 <param name="keep" value="1"/>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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diff changeset
426 <output name="assembly_graph" ftype="gfa1">
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iuc
parents: 8
diff changeset
427 <assert_contents>
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iuc
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diff changeset
428 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/>
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iuc
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429 </assert_contents>
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diff changeset
430 </output>
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iuc
parents: 8
diff changeset
431 <output name="assembly" ftype="fasta">
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diff changeset
432 <assert_contents>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
433 <has_text text="length=5386" />
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
434 </assert_contents>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
435 </output>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
436 <output_collection name="spades_collection" type="list" count="14">
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
437 <element name="001_spades_graph_k027">
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
438 <assert_contents>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
439 <has_text text="TTGAATGCCACCGGAGGCGGCTTTTTGACCGCCTCCAAAC"/>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
440 </assert_contents>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
441 </element>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
442 </output_collection>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
443 </test>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
444 <!-- Test keep value = 2 -->
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
445 <test expect_num_outputs="4">
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
446 <conditional name="paired_unpaired">
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
447 <param name="fastq_input_selector" value="paired" />
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
448 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" />
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
449 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" />
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
450 </conditional>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
451 <param name="long" value="onp.fa" ftype="fasta" />
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
452 <param name="mode" value="normal" />
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
453 <param name="keep" value="2"/>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
454 <output name="assembly_graph" ftype="gfa1">
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
455 <assert_contents>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
456 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
457 </assert_contents>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
458 </output>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
459 <output name="assembly" ftype="fasta">
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
460 <assert_contents>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
461 <has_text text="length=5386" />
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
462 </assert_contents>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
463 </output>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
464 <output_collection name="spades_collection" type="list" count="14">
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
465 <element name="001_spades_graph_k027">
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
466 <assert_contents>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
467 <has_text text="TTGAATGCCACCGGAGGCGGCTTTTTGACCGCCTCCAAAC"/>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
468 </assert_contents>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
469 </element>
11
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
470 <!-- there are gfa files for more k that are not tested explicily
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
471 Aim of testing these is to be sure about the names of the graphs,
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
472 since they are used for reuse. Hence if there is a change here
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
473 update reuse accordingly-->
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
474 <element name="001_spades_graph_k127">
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
475 <assert_contents>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
476 <has_line_matching expression="^S.*"/>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
477 </assert_contents>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
478 </element>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
479 <element name="002_depth_filter">
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
480 <assert_contents>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
481 <has_line_matching expression="^S.*"/>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
482 </assert_contents>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
483 </element>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
484 <element name="003_overlaps_removed">
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
485 <assert_contents>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
486 <has_line_matching expression="^S.*"/>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
487 </assert_contents>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
488 </element>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
489 <element name="004_bridges_applied">
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
490 <assert_contents>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
491 <has_line_matching expression="^S.*"/>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
492 </assert_contents>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
493 </element>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
494 <element name="005_final_clean">
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
495 <assert_contents>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
496 <has_line_matching expression="^S.*"/>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
497 </assert_contents>
8f9f06995f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents: 10
diff changeset
498 </element>
9
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
499 </output_collection>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
500 <output name="bam_file" ftype="bam">
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
501 <assert_contents>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
502 <has_size value="2084" delta="100"/>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
503 </assert_contents>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
504 </output>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
505 </test>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
506 <!-- Test no simple bridges option -->
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
507 <test expect_num_outputs="2">
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
508 <conditional name="paired_unpaired">
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
509 <param name="fastq_input_selector" value="paired" />
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
510 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" />
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
511 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" />
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
512 </conditional>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
513 <param name="long" value="onp.fa" ftype="fasta" />
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
514 <param name="mode" value="normal" />
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
515 <param name="keep" value="0"/>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
516 <section name="lr_align">
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
517 <param name="no_simple_bridges" value="true"/>
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents: 8
diff changeset
518 </section>
8
9e3e80cc4ad4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d7f4eb848136b02ae1cf121a5cfb2e6175d35406"
iuc
parents: 7
diff changeset
519 <output name="assembly_graph" ftype="gfa1">
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
520 <assert_contents>
8
9e3e80cc4ad4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d7f4eb848136b02ae1cf121a5cfb2e6175d35406"
iuc
parents: 7
diff changeset
521 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/>
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
522 </assert_contents>
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
523 </output>
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524 <output name="assembly" ftype="fasta">
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
525 <assert_contents>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
526 <has_text text="length=5386" />
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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527 </assert_contents>
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528 </output>
9
6e26c9afd301 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
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diff changeset
529 <assert_command>
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diff changeset
530 <has_text text="--no_simple_bridges" />
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531 </assert_command>
4
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532 </test>
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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533 </tests>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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534 <help><![CDATA[
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
535
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
536 **Unicycler**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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537
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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538 Unicycler is a hybrid assembly pipeline for bacterial genomes. It uses both Illumina reads and long reads (PacBio or Nanopore) to produce complete and accurate assemblies. It is written by `Ryan Wick`_ at the University of Melbourne's Centre for Systems Genomics. Much of the description below is lifted from Unicycler's `github page`_.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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539
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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540 .. _`Ryan Wick`: https://github.com/rrwick
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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541 .. _`github page`: https://github.com/rrwick/Unicycler
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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542
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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543 -----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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544
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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545 **Input data**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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546
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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547 Unicycler accepts inputs short (Illumina) reads in FASTQ format. Galaxy places additional requirement of having these in FASTQ format with `Sanger encoding`_ of quality scores. Long reads (from Oxford Nanopore or PacBio) can be either in FASTQ of FASTA form.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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548
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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549 .. _`Sanger encoding`: https://en.wikipedia.org/wiki/FASTQ_format#Quality
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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550
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551 The input options are::
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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552
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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553 -1 SHORT1, --short1 SHORT1
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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554 FASTQ file of short reads (first reads in each pair)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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555 -2 SHORT2, --short2 SHORT2
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
556 FASTQ file of short reads (second reads in each pair)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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557 -s SHORT_UNPAIRED, --short_unpaired SHORT_UNPAIRED
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diff changeset
558 FASTQ file of unpaired short reads
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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559 -l LONG, --long LONG
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
560 FASTQ or FASTA file of long reads, if all reads are available at start.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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561
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562 -----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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563
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564 **Bridging mode**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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565
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
566 Unicycler can be run in three modes: conservative, normal (the default) and bold, set with the --mode option. Conservative mode is least likely to produce a complete assembly but has a very low risk of misassembly. Bold mode is most likely to produce a complete assembly but carries greater risk of misassembly. Normal mode is intermediate regarding both completeness and misassembly risk. See `description of modes`_ for more information.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
567
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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568 .. _`description of modes`: https://github.com/rrwick/Unicycler#conservative-normal-and-bold
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
569
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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570 The available modes are::
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
571
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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572 --mode {conservative,normal,bold}
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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573 Bridging mode (default: normal)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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574 conservative = smaller contigs, lowest misassembly rate
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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575 normal = moderate contig size and misassembly rate
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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576 bold = longest contigs, higher misassembly rate
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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577
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578 ----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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579
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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580 **Skip SPAdes error correction step**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
581
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
582 Sequencing data contains a substantial number of sequencing errors that manifest themselves as deviations (bulges and non-connected components) within the assembly graph. One of the ways to improve the graph even constructing it is to minimize the amount sequencing errors by performing error correction. SPAdes, which is used by Unicycler for error correction and assembly, uses `BayesHammer`_ to correct the reads. Here is a brief summary of what it does:
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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583
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
584 1. SPAdes (or rather BayesHammer) counts *k*-mers in reads and computed *k*-mer statistics that takes into account base quality values.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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585 2. `Hamming graph`_ is constructed for *k*-mers is which *k*-mers are nodes. In this graph edges connect nodes (*k*-mers) is they differ from each other by a number of nucleotides up to a certain threshold (the `Hamming distance`_). The graph is central to the error correction algorithm.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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586 3. At this step Bayesian subclustering of the graph produced in the previous step. For each *k*-mer we now know the center of its subcluster.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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587 4. Solid *k*-mers are derived from cluster centers and are assumed to be *error free*.
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588 5. Solid *k*-mers are mapped back to the reads and used to correct them.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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589
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590 This step takes considerable time, so if one need to quickly evaluate assemblies this step can be skipped. However, this is not recommended if one if trying to produce a final high quality assembly.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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591
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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592 .. _`BayesHammer`: https://goo.gl/1iGkMe
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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593 .. _`Hamming graph`: https://en.wikipedia.org/wiki/Hamming_graph
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594 .. _`Hamming distance`: https://en.wikipedia.org/wiki/Hamming_distance
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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595
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596
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597 -----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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598
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599 **Do not rotate completed replicons to start at a standard gene**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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600
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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601 Unicycler uses TBLASTN to search for dnaA or repA alleles in each completed replicon. If one is found, the sequence is rotated and/or flipped so that it begins with that gene encoded on the forward strand. This provides consistently oriented assemblies and reduces the risk that a gene will be split across the start and end of the sequence.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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602
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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603 The following option turns rotation on and off::
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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604
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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605 --no_rotate
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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606 Do not rotate completed replicons
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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607 to start at a standard gene
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
608 (default: completed replicons are rotated)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
609
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
610 **Do not use Pilon to polish the final assembly**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
611
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
612 `Pilon`_ is a tool for improving overall quality of draft assemblies and finding variation among strains. Unicycler uses it for assembly *polishing*.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
613
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
614 The following option turns pilon part of Unicycler pipeline on and off::
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
615
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
616 --no_pilon
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
617 Do not use Pilon to polish the
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
618 final assembly (default: Pilon is used)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
619
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
620 .. _`Pilon`: https://github.com/broadinstitute/pilon/wiki
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
621
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
622 ------
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
623
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
624 **Expected number of linear sequences**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
625
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
626 If you expect your sample to contain linear (non circular) sequences, set this option::
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
627
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
628 --linear_seqs EXPECTED_LINEAR_SEQS
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
629 The expected number of linear (i.e. non-circular)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
630 sequences in the underlying sequence
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
631
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
632 ----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
633
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
634 **SPAdes options**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
635
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
636 This section provides control of SPAdes options::
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
637
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
638 --min_kmer_frac MIN_KMER_FRAC
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
639 Lowest k-mer size for SPAdes assembly,
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
640 expressed as a fraction of the read length
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
641 (default: 0.2)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
642 --max_kmer_frac MAX_KMER_FRAC
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
643 Highest k-mer size for SPAdes assembly,
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
644 expressed as a fraction of the read length
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
645 (default: 0.95)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
646 --kmer_count KMER_COUNT
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
647 Number of k-mer steps to use in
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
648 SPAdes assembly (default: 10)
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
649 --depth_filter DEPTH_FILTER
4
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
650 Filter out contigs lower than this fraction
2db911a4efc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
651 of the chromosomal depth, if doing so does
2
e92675014ac9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
652 not result in graph dead ends (default: 0.25)
0
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
653
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
654 ----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
655
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
656 **Rotation options**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
657
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
658 Unicycler attempts to rotate circular assemblies to make sure that they begin at a consistent starting gene. The following parameters control assembly rotation::
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
659
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
660 --start_genes START_GENES
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
661 FASTA file of genes for start point
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
662 of rotated replicons
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
663 (default: start_genes.fasta)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
664 --start_gene_id START_GENE_ID
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
665 The minimum required BLAST percent identity
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
666 for a start gene search
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
667 (default: 90.0)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
668 --start_gene_cov START_GENE_COV
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
669 The minimum required BLAST percent coverage
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
670 for a start gene search
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
671 (default: 95.0)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
672
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
673 -----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
674
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
675 **Graph cleaning options**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
676
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
677 These options control the removal of small leftover sequences after bridging is complete::
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
678
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
679 --min_component_size MIN_COMPONENT_SIZE
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
680 Unbridged graph components smaller
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
681 than this size (bp) will be removed
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
682 from the final graph (default: 1000)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
683 --min_dead_end_size MIN_DEAD_END_SIZE
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
684 Graph dead ends smaller than this size (bp)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
685 will be removed from the final graph
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
686 (default: 1000)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
687
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
688 -----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
689
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
690 **Long read alignment options**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
691
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
692 These options control the alignment of long reads to the assembly graph::
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
693
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
694 --contamination CONTAMINATION
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
695 FASTA file of known contamination in long reads
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
696 --scores SCORES
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
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697 Comma-delimited string of alignment scores:
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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698 match, mismatch, gap open, gap extend
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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699 (default: 3,-6,-5,-2)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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700 --low_score LOW_SCORE
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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701 Score threshold - alignments below this
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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702 are considered poor
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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703 (default: set threshold automatically)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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704
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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705 -----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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706
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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707 **Outputs**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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708
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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709 Galaxy's wrapped for Unicycler produces two outputs:
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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710
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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711 * final assembly in FASTA format
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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712 * final assembly grapth in graph format
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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713
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714 While most will likely be interested in the FASTA dataset, the graph dataset is also quite useful and can be visualized using tools such as `Bandage`_.
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715
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716
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717 .. _`Bandage`: https://github.com/rrwick/Bandage
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718
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719
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720 ]]></help>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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721 <citations>
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722 <citation type="doi">10.1101/096412</citation>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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723 </citations>
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724 </tool>