Mercurial > repos > peterjc > mira_assembler

annotate tools/mira3/mira.xml @ 12:63ebe9726219 draft default tip

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v0.0.11 move dependency to package_mira_3_4_1_1 etc
author peterjc
date Wed, 05 Aug 2015 11:28:05 -0400
parents e59904c855ae
children
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63ebe9726219 v0.0.11 move dependency to package_mira_3_4_1_1 etc
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1 <tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.11">
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2 <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
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3 <requirements>
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4 <requirement type="binary">mira</requirement>
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5 <requirement type="package" version="3.4.1.1">MIRA</requirement>
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6 </requirements>
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7 <version_command interpreter="python">mira.py -v</version_command>
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8 <command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log
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9 ##Give the wrapper script list of output filenames, then the mira command...
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10 mira --job=$job_method,$job_type,$job_quality
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11
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12 ##Input files
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13 #if $condBackbone.use == "true":
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14 ## Can this be linked to job_method as well? If mapping we need the backbone...
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15 -SB:lb=1:bft=fasta -FN:bbin=${condBackbone.filename}
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16 #end if
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17 #if $condSanger.use == "true":
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18 SANGER_SETTINGS
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19 ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead
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20 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
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21 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename}
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22 #end if
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23 #if $condRoche.use == "true":
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24 454_SETTINGS
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25 ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead
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26 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
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27 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condRoche.filename}
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28 #end if
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29 #if $condIllumina.use == "true":
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30 SOLEXA_SETTINGS
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31 ## Not easy in Galaxy to add solexa to --job, so use load_sequence_data(lsd) instead
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32 -LR:lsd=1:ft=fastq -FN:fqi=${condIllumina.filename}
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33 ##TODO - Look at -LR FASTQ qual offset (fqqo)
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34 #end if
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35 #if $condIonTorrent.use == "true":
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36 IONTOR_SETTINGS
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37 ## Not easy in Galaxy to add iontor to --job, so use load_sequence_data(lsd) instead
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38 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
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39 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condIonTorrent.filename}
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40 #end if
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41
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42 ##Output files
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43 COMMON_SETTINGS
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44
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45 ##ignore warnings about long read names
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46 -MI:somrnl=0
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47
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48 ##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output
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49 ##Explicitly disable formats we won't use like MAF (reduce IO)
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50 -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0
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51
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52 ##remove_rollover_tmps, remove_tmp_directory
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53 -OUT:rrot=1:rtd=1
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54
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55 ##put mira temp directory on local storage
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56 -DI:trt=/tmp
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57
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58 </command>
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59 <inputs>
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60 <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)">
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61 <option value="denovo">De novo</option>
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62 <option value="mapping">Mapping</option>
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63 </param>
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64 <param name="job_type" type="select" label="Assembly type">
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65 <option value="genome">Genome</option>
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66 <option value="est">EST (transcriptome)</option>
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67 </param>
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68 <param name="job_quality" type="select" label="Assembly quality grade">
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69 <option value="accurate">Accurate</option>
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70 <option value="normal">Normal (deprecated)</option>
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71 <option value="draft">Draft</option>
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72 </param>
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73 <!-- Backbone -->
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74 <conditional name="condBackbone">
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75 <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly.">
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76 <option value="false">No</option>
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77 <option value="true">Yes</option>
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78 </param>
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79 <when value="false" />
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80 <when value="true">
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81 <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) -->
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82 <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" />
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83 </when>
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84 </conditional>
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85 <!-- Sanger -->
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86 <conditional name="condSanger">
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87 <param name="use" type="select" label="Sanger/Capillary reads?">
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88 <option value="false">No</option>
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89 <option value="true">Yes</option>
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90 </param>
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91 <when value="false" />
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92 <when value="true">
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93 <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" />
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94 </when>
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95 </conditional>
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96 <!-- Roche 454 -->
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97 <conditional name="condRoche">
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98 <param name="use" type="select" label="454 reads?">
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99 <option value="false">No</option>
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100 <option value="true">Yes</option>
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101 </param>
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102 <when value="false" />
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103 <when value="true">
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104 <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences -->
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105 <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" />
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106 </when>
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107 </conditional>
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108 <!-- Illumina -->
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109 <conditional name="condIllumina">
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110 <param name="use" type="select" label="Solexa/Illumina reads?">
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111 <option value="false">No</option>
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112 <option value="true">Yes</option>
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113 </param>
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114 <when value="false" />
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115 <when value="true">
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116 <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" />
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117 </when>
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118 </conditional>
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119 <!-- Ion Torrent -->
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120 <conditional name="condIonTorrent">
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121 <param name="use" type="select" label="Ion Torrent reads?">
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122 <option value="false">No</option>
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123 <option value="true">Yes</option>
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124 </param>
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125 <when value="false" />
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126 <when value="true">
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127 <!-- TODO? Support SFF files directly, e.g. with sff_extract -->
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128 <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" />
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129 </when>
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130 </conditional>
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131 </inputs>
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132 <outputs>
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133 <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" />
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134 <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" />
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135 <data name="out_caf" format="txt" label="MIRA contigs (CAF)" />
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136 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
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137 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
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138 <data name="out_log" format="txt" label="MIRA log" />
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139 </outputs>
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140 <tests>
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141 <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses
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142 strain data and miraSearchESTSNPs. Here we just assemble it. -->
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143 <test>
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144 <param name="job_method" value="denovo" />
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145 <param name="job_type" value="est" />
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146 <param name="job_qual" value="accurate" />
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147 <param name="condBackbone|use" value="false" />
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148 <param name="condSanger|use" value="true" />
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149 <param name="condSanger|filename" value="tvc_mini.fastq" ftype="fastq" />
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150 <param name="condRoche|use" value="false" />
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151 <param name="condIllumina|use" value="false" />
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152 <param name="condIonTorrent|use" value="false" />
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153 <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />
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154 <output name="out_qual" file="empty_file.dat" compare="contains" />
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155 <output name="out_caf" file="empty_file.dat" compare="contains" />
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156 <output name="out_ace" file="empty_file.dat" compare="contains" />
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157 <output name="out_wig" file="empty_file.dat" compare="contains" />
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158 <output name="out_log" file="empty_file.dat" compare="contains" />
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159 </test>
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160 </tests>
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161 <help>
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162
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163 **What it does**
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164
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165 Runs MIRA v3.4, collects the output, and throws away all the temporary files.
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166
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167 MIRA is an open source assembly tool capable of handling sequence data from
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168 a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454 and also
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169 Ion Torrent).
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170
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171 It is particularly suited to small genomes such as bacteria.
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172
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173 **Citation**
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174
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175 If you use this Galaxy tool in work leading to a scientific publication please
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176 cite the following papers:
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177
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178 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
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179 Galaxy tools and workflows for sequence analysis with applications
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180 in molecular plant pathology. PeerJ 1:e167
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181 http://dx.doi.org/10.7717/peerj.167
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182
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183 Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999).
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184 Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
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185 Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
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186 http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html
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187
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188 This wrapper is available to install into other Galaxy Instances via the Galaxy
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189 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
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190
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191 </help>
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192 <citations>
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193 <citation type="doi">10.7717/peerj.167</citation>
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194 <citation type="bibtex">@ARTICLE{Chevreux1999-mira3,
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195 author = {B. Chevreux and T. Wetter and S. Suhai},
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196 year = {1999},
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197 title = {Genome Sequence Assembly Using Trace Signals and Additional Sequence Information},
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198 journal = {Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB)}
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199 volume = {99},
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200 pages = {45-56},
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201 url = {http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html}
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202 }</citation>
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203 </citations>
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204 </tool>