Mercurial > repos > peterjc > mira4_assembler

annotate tools/mira4/mira4_de_novo.xml @ 10:79759fdec6cb draft

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Uploaded v0.0.2 preview 2, attempt auto-install for 64 bit Mac OS X.
author peterjc
date Tue, 10 Dec 2013 06:26:19 -0500
parents 302d13490b23
children 7fcabeeca5df
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1 <tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.2">
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2 <description>Takes Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description>
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3 <requirements>
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4 <requirement type="binary">mira</requirement>
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5 <requirement type="binary">miraconvert</requirement>
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6 <requirement type="package" version="4.0">MIRA</requirement>
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7 <requirement type="binary">samtools</requirement>
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8 <requirement type="package" version="0.1.19">samtools</requirement>
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9 </requirements>
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10 <version_command interpreter="python">mira4.py --version</version_command>
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11 <command interpreter="python">
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12 mira4.py "$manifest" "$out_maf" "$out_bam" "$out_fasta" "$out_log"
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13 </command>
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14 <stdio>
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15 <!-- Assume anything other than zero is an error -->
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16 <exit_code range="1:" />
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17 <exit_code range=":-1" />
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18 </stdio>
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19 <inputs>
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20 <param name="job_type" type="select" label="Assembly type">
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21 <option value="genome">Genome</option>
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22 <option value="est">EST (transcriptome)</option>
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23 </param>
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24 <param name="job_quality" type="select" label="Assembly quality grade">
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25 <option value="accurate">Accurate</option>
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26 <option value="draft">Draft</option>
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27 </param>
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28 <repeat name="read_group" title="Read Group" min="1">
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29 <param name="technology" type="select" label="Read technology">
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30 <option value="solexa">Solexa/Illumina</option>
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31 <option value="sanger">Sanger cappillary sequencing</option>
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32 <option value="454">Roche 454</option>
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33 <option value="iontor">Ion Torrent</option>
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34 <option value="pcbiolq">PacBio low quality (raw)</option>
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35 <option value="pcbiohq">PacBio high quality (corrected)</option>
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36 <option value="text">Synthetic reads (database entries, consensus sequences, artifical reads, etc)</option>
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37 <!-- TODO reference/backbone as an entry here? -->
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38 </param>
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39 <conditional name="segments">
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40 <param name="type" type="select" label="Are these paired reads?">
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41 <option value="paired">Paired reads</option>
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42 <option value="none">Single reads or not relevant (e.g. primer walking with Sanger capillary sequencing)</option>
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43 </param>
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44 <when value="paired">
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45 <param name="placement" type="select" label="Pairing type (segment placing)">
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46 <option value="FR">---&gt; &lt;--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option>
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47 <option value="RF">&lt;--- ---&gt; (e.g. Solexa/Illumina mate-pair library)</option>
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48 <option value="SB">2---&gt; 1---&gt; (e.g. Roche 454 paired-end libraries or IonTorrent long-mate; see note)</option>
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49 </param>
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50 <!-- min/max validation is done via the <code> tag -->
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51 <param name="min_size" type="integer" optional="true" min="0" value=""
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52 label="Minimum size of 'good' DNA templates in the library preparation"
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53 help="Optional, but if used you must also supply a maximum value." />
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54 <param name="max_size" type="integer" optional="true" min="0" value=""
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55 label="Maximum size of 'good' DNA templates in the library preparation"
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56 help="Optional, but if used you must also supply a minimum value." />
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57 <param name="naming" type="select" label="Pair naming convention">
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58 <option value="solexa">Solexa/Illumina (using '/1' and '/2' suffixes, or later Illumina colon system)</option>
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59 <option value="FR">Forward/Reverse scheme (using '.f*' and '.r*' suffixes)</option>
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60 <option value="tigr">TIGR scheme (using 'TF*' and 'TR*' suffixes)</option>
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61 <option value="sanger">Sanger scheme (see notes)</option>
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62 <option value="stlouis">St. Louis scheme (see notes)</option>
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63 </param>
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64 </when>
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65 <when value="none" /><!-- no further questions -->
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66 </conditional>
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67 <param name="filenames" type="data" format="fastq,mira" multiple="true" required="true" label="Read file(s)"
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68 help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." />
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69 </repeat>
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70 </inputs>
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71 <code file="mira4_validator.py" />
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72 <outputs>
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73 <data name="out_fasta" format="fasta" label="MIRA de novo contigs (FASTA)" />
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74 <data name="out_bam" format="bam" label="MIRA de novo assembly (BAM)" />
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75 <data name="out_maf" format="mira" label="MIRA de novo assembly" />
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76 <data name="out_log" format="txt" label="MIRA de novo log" />
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77 </outputs>
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78 <configfiles>
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79 <configfile name="manifest">
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80 project = MIRA
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81 job = denovo,${job_type},${job_quality}
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82 parameters = -GE:not=1 -NW:cmrnl -DI:trt=/tmp
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83 ## -GE:not is short for -GENERAL:number_of_threads and using one (1)
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84 ## can be useful for repeatability of assemblies and bug hunting.
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85 ##
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86 ## -NW:cmrnl is short for -NAG_AND_WARN:check_maxreadnamelength
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87 ## and without this MIRA aborts with read names over 40 characters
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88 ## due to limitations of some downstream tools.
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89 ##
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90 ## -DI:trt is short for -DIRECTORY:tmp_redirected_to and should
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91 ## point to a local hard drive (not something like NFS on network).
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92
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93 #for $rg in $read_group
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94
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95 ##This bar goes into the manifest as a comment line
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96 #------------------------------------------------------------------------------
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97
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98 readgroup
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99 technology = ${rg.technology}
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100 ##Record the segment placement (if any)
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101 #if str($rg.segments.type) == "paired"
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102 segmentplacement = ${rg.segments.placement}
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103 segmentnaming = ${rg.segments.naming}
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104 #if str($rg.segments.min_size) != "" or str($rg.segments.max_size) != ""
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105 ##If our min/max validation failed I trust MIRA to give an error message...
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106 templatesize = $rg.segments.min_size $rg.segments.max_size
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107 #end if
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108 #end if
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109 #if str($rg.segments.type) == "none"
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110 segmentplacement = ?
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111 #end if
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112 ##MIRA will accept multiple filenames on one data line, or multiple data lines
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113 #for $f in $rg.filenames
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114 ##Must now map Galaxy datatypes to MIRA file types...
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115 #if $f.ext.startswith("fastq")
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116 ##MIRA doesn't like fastqsanger etc, just plain old fastq:
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117 data = fastq::$f
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118 #elif $f.ext == "mira"
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119 ##We're calling *.maf the "mira" format in Galaxy (name space collision)
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120 data = maf::$f
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121 #else
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122 ##MIRA is happy with fasta as name,
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123 data = ${f.ext}::$f
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124 #end if
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125 #end for
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126 #end for
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127 </configfile>
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128 </configfiles>
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129 <tests>
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130 <!-- Tiger mitochondria, selected paired end Illumina reads from SRR639755
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131 Note we're using just one repeat group, and only the filenames parameter
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132 within it, so this should work with current test framework limitations:
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133 <test>
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134 <param name="job_type" value="genome" />
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135 <param name="job_quality" value="accurate" />
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136 <param name="filenames" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" />
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137 <output name="out_fasta" file="SRR639755_mito_pairs.mira4_de_novo.fasta" ftype="fasta" />
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138 </test>
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139 -->
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140 <!-- Simple assembly based on MIRA's minidemo/demo4 example
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141 Note we're using just one repeat group,
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142 but several parameters with the repeat
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143 (in order to specify sanger reads, no pairing)
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144 <test>
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145 <param name="job_type" value="genome" />
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146 <param name="job_quality" value="accurate" />
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147 <param name="technology" value="sanger" />
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148 <param name="type" value="none" />
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149 <param name="filenames" value="U13small_m.fastq" ftype="fastqsanger" />
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150 <output name="out_fasta" file="U13small_m.mira4_de_novo.fasta" ftype="fasta" />
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151 </test>
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152 -->
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153 <!-- Simple assembly based on MIRA's minidemo/solexa1 example
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154 Note we're using just one repeat group,
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155 but two parameters within the repeat (filename, no pairing)
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156 <test>
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157 <param name="job_type" value="genome" />
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158 <param name="job_quality" value="accurate" />
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159 <param name="type" value="none" />
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160 <param name="filenames" value="ecoli.fastq" ftype="fastqsanger" />
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161 <output name="out_fasta" file="ecoli.mira4_de_novo.fasta" ftype="fasta" />
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162 </test>
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163 -->
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164 </tests>
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165 <help>
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166
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167 **What it does**
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168
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169 Runs MIRA v4.0 in de novo mode, collects the output, generates a sorted BAM
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170 file, and then throws away all the temporary files.
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171
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172 MIRA is an open source assembly tool capable of handling sequence data from
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173 a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454, Ion Torrent
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174 and also PacBio).
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175
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176 It is particularly suited to small genomes such as bacteria.
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177
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178
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179 **Notes on paired reads**
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180
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181 .. class:: warningmark
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182
6
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183 MIRA uses read naming conventions to identify paired read partners
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184 (and does not care about their order in the input files). In most cases,
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185 the Solexa/Illumina setting is fine. For Sanger capillary sequencing,
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186 you may need to rename your reads to match one of the standard conventions
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187 supported by MIRA. For Roche 454 or Ion Torrent the appropriate settings
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188 depend on how the FASTQ file was produced:
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189
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190 * If using Roche's ``sffinfo`` or older versions of ``sff_extract``
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191 to convert SFF files to FASTQ, your reads will probably have the
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192 ``---&gt; &lt;---`` orientation and use the ``.f`` and ``.r``
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193 suffixes (FR naming).
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194
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195 * If using a recent version of ``sff_extract``, then the ``/1`` and ``/2``
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196 suffixes are used (Solexa/Illumina style naming) and the original
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197 ``2---&gt; 1---&gt;`` orientation is preserved.
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198
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199 The reason for this is the raw data for Roche 454 and Ion Torrent paired-end
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200 libraries sequences a circularised fragment such that the raw data begins
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201 with the end of the fragment, a linker, then the start of the fragment.
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202 This means both the start and end are sequenced from the same strand, and
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203 have the orientation ``2---&gt; 1---&gt;``. However, in order to use the data
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204 with traditional tools expecting Sanger capillary style ``---&gt; &lt;---``
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205 orientation it was common to reverse complement one of the pair to mimic this.
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206
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207
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208 **Citation**
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209
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210 If you use this Galaxy tool in work leading to a scientific publication please
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211 cite the following papers:
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212
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213 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
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214 Galaxy tools and workflows for sequence analysis with applications
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215 in molecular plant pathology. PeerJ 1:e167
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216 http://dx.doi.org/10.7717/peerj.167
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217
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218 Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999).
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219 Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
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220 Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
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221 http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html
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222
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223 This wrapper is available to install into other Galaxy Instances via the Galaxy
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224 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
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225 </help>
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226 </tool>