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1 <tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.4">
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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">mira4.py
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12 --manifest "$manifest"
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13 #if str($maf_wanted)=="true":
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14 --maf "$out_maf"
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15 #end if
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16 #if str($bam_wanted)=="true":
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17 --bam "$out_bam"
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18 #end if
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19 --fasta "$out_fasta"
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20 --log "$out_log"
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21 </command>
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22 <stdio>
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23 <!-- Assume anything other than zero is an error -->
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24 <exit_code range="1:" />
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25 <exit_code range=":-1" />
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26 </stdio>
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27 <inputs>
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28 <param name="job_type" type="select" label="Assembly type">
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29 <option value="genome">Genome</option>
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30 <option value="est">EST (transcriptome)</option>
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31 </param>
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32 <param name="job_quality" type="select" label="Assembly quality grade">
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33 <option value="accurate">Accurate</option>
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34 <option value="draft">Draft</option>
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35 </param>
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36 <repeat name="read_group" title="Read Group" min="1">
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37 <param name="technology" type="select" label="Read technology">
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38 <option value="solexa">Solexa/Illumina</option>
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39 <option value="sanger">Sanger cappillary sequencing</option>
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40 <option value="454">Roche 454</option>
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41 <option value="iontor">Ion Torrent</option>
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42 <option value="pcbiolq">PacBio low quality (raw)</option>
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43 <option value="pcbiohq">PacBio high quality (corrected)</option>
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44 <option value="text">Synthetic reads (database entries, consensus sequences, artifical reads, etc)</option>
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45 <!-- TODO reference/backbone as an entry here? -->
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46 </param>
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47 <conditional name="segments">
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48 <param name="type" type="select" label="Are these paired reads?">
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49 <option value="paired">Paired reads</option>
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50 <option value="none">Single reads or not relevant (e.g. primer walking with Sanger capillary sequencing)</option>
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51 </param>
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52 <when value="paired">
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53 <param name="placement" type="select" label="Pairing type (segment placing)">
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54 <option value="FR">---> <--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option>
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55 <option value="RF"><--- ---> (e.g. Solexa/Illumina mate-pair library)</option>
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56 <option value="SB">2---> 1---> (e.g. Roche 454 paired-end libraries or IonTorrent long-mate; see note)</option>
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57 </param>
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58 <!-- min/max validation is done via the <code> tag -->
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59 <param name="min_size" type="integer" optional="true" min="0" value=""
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60 label="Minimum size of 'good' DNA templates in the library preparation"
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61 help="Optional, but if used you must also supply a maximum value." />
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62 <param name="max_size" type="integer" optional="true" min="0" value=""
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63 label="Maximum size of 'good' DNA templates in the library preparation"
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64 help="Optional, but if used you must also supply a minimum value." />
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65 <param name="naming" type="select" label="Pair naming convention">
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66 <option value="solexa">Solexa/Illumina (using '/1' and '/2' suffixes, or later Illumina colon system)</option>
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67 <option value="FR">Forward/Reverse scheme (using '.f*' and '.r*' suffixes)</option>
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68 <option value="tigr">TIGR scheme (using 'TF*' and 'TR*' suffixes)</option>
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69 <option value="sanger">Sanger scheme (see notes)</option>
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70 <option value="stlouis">St. Louis scheme (see notes)</option>
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71 </param>
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72 </when>
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73 <when value="none" /><!-- no further questions -->
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74 </conditional>
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75 <param name="filenames" type="data" format="fastq,mira" multiple="true" required="true" label="Read file(s)"
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76 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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77 </repeat>
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78 <param name="maf_wanted" type="boolean" label="Output assembly in MIRA's own format?" checked="False" />
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79 <param name="bam_wanted" type="boolean" label="Convert assembly into BAM format?" checked="True" />
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80 </inputs>
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81 <code file="mira4_validator.py" />
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82 <outputs>
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83 <data name="out_fasta" format="fasta" label="MIRA de novo contigs (FASTA)" />
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84 <data name="out_bam" format="bam" label="MIRA de novo assembly (BAM)">
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85 <filter>bam_wanted is True</filter>
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86 </data>
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87 <data name="out_maf" format="mira" label="MIRA de novo assembly">
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88 <filter>maf_wanted is True</filter>
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89 </data>
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90 <!-- TODO?
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91 <data name="out_contigstats" format="tabular" label="MIRA contig stats" />
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92 -->
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93 <data name="out_log" format="txt" label="MIRA de novo log" />
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94 </outputs>
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95 <configfiles>
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96 <configfile name="manifest">
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97 project = MIRA
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98 job = denovo,${job_type},${job_quality}
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99 parameters = -NW:cmrnl=no -DI:trt=/tmp -OUT:orc=no
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100 ## -GE:not is short for -GENERAL:number_of_threads and using one (1)
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101 ## can be useful for repeatability of assemblies and bug hunting.
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102 ## This is overriden by the command line -t switch which is easier
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103 ## to set from within Galaxy.
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104 ##
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105 ## -NW:cmrnl is short for -NAG_AND_WARN:check_maxreadnamelength
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106 ## and without this MIRA aborts with read names over 40 characters
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107 ## due to limitations of some downstream tools.
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108 ##
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109 ## -DI:trt is short for -DIRECTORY:tmp_redirected_to and should
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110 ## point to a local hard drive (not something like NFS on network).
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111 ## We replace /tmp with an environment variable via mira4.py
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112 ##
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113 ## -OUT:orc=no is short for -OUTPUT:output_result_caf=no
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114 ## which turns off an output file we don't want anyway.
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115
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116 #for $rg in $read_group
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117
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118 ##This bar goes into the manifest as a comment line
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119 #------------------------------------------------------------------------------
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120
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121 readgroup
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122 technology = ${rg.technology}
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123 ##Record the segment placement (if any)
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124 #if str($rg.segments.type) == "paired"
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125 segment_placement = ${rg.segments.placement}
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126 segment_naming = ${rg.segments.naming}
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127 #if str($rg.segments.min_size) != "" or str($rg.segments.max_size) != ""
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128 ##If our min/max validation failed I trust MIRA to give an error message...
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129 template_size = $rg.segments.min_size $rg.segments.max_size
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130 #end if
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131 #end if
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132 ##if str($rg.segments.type) == "none"
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133 ##MIRA4 manual says use segment_placement = unknown or ? for unpaired data
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134 ##but this stopped working in MIRA 4.0 RC5 and 4.0 (final). See:
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135 ##http://www.freelists.org/post/mira_talk/Unpaired-reads-and-segment-placement--or-unknown
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136 ##segment_placement = ?
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137 ##end if
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138 ##MIRA will accept multiple filenames on one data line, or multiple data lines
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139 #for $f in $rg.filenames
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140 ##Must now map Galaxy datatypes to MIRA file types...
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141 #if $f.ext.startswith("fastq")
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142 ##MIRA doesn't like fastqsanger etc, just plain old fastq:
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143 data = fastq::$f
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144 #elif $f.ext == "mira"
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145 ##We're calling *.maf the "mira" format in Galaxy (name space collision)
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146 data = maf::$f
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147 #else
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148 ##MIRA is happy with fasta as name,
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149 data = ${f.ext}::$f
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150 #end if
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151 #end for
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152 #end for
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153 </configfile>
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154 </configfiles>
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155 <tests>
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156 <!-- Tiger mitochondria, selected paired end Illumina reads from SRR639755
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157 Note we're using just one repeat group, and only the filenames parameter
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158 within it, so this should work with current test framework limitations:
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159 TODO: Revise example and/or -NW:cac=warn and -NW:acv=80 settings
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160 MIRA 4.0 complains as coverage is about x93 which is over 80 limit.
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161 Also MIRA 4.0 gives three contigs as output.
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162 <test>
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163 <param name="job_type" value="genome" />
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164 <param name="job_quality" value="accurate" />
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165 <param name="filenames" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" />
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166 <output name="out_fasta" file="SRR639755_mito_pairs.mira4_de_novo.fasta" ftype="fasta" />
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167 </test>
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168 -->
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169 <!-- Simple assembly based on MIRA's minidemo/demo4 example
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170 Note we're using just one repeat group,
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171 but several parameters with the repeat
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172 -->
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173 <test>
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174 <param name="job_type" value="genome" />
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175 <param name="job_quality" value="accurate" />
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176 <param name="technology" value="sanger" />
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177 <param name="type" value="none" />
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178 <param name="filenames" value="U13small_m.fastq" ftype="fastqsanger" />
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179 <param name="maf_wanted" value="true"/>
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180 <param name="bam_wanted" value="true"/>
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181 <output name="out_fasta" file="U13small_m.mira4_de_novo.fasta" ftype="fasta" />
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182 <output name="out_bam" file="empty_file.dat" compare="contains" />
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183 <!-- TODO: Suggest startswith as a compare method? -->
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184 <output name="out_maf" file="header.mira" compare="contains" />
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185 <output name="out_log" file="empty_file.dat" compare="contains" />
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186 </test>
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187 <!-- Simple assembly based on MIRA's minidemo/solexa1 example
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188 Note we're using just one repeat group,
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189 but two parameters within the repeat (filename, no pairing)
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190 -->
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191 <test>
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192 <param name="job_type" value="genome" />
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193 <param name="job_quality" value="accurate" />
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194 <param name="type" value="none" />
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195 <param name="filenames" value="ecoli.fastq" ftype="fastqsanger" />
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196 <param name="maf_wanted" value="false"/>
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197 <param name="bam_wanted" value="false"/>
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198 <output name="out_fasta" file="ecoli.mira4_de_novo.fasta" ftype="fasta" />
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199 <output name="out_log" file="empty_file.dat" compare="contains" />
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200 </test>
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201 </tests>
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202 <help>
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203
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204 **What it does**
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205
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206 Runs MIRA v4.0 in de novo mode, collects the output, generates a sorted BAM
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207 file, and then throws away all the temporary files.
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208
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209 MIRA is an open source assembly tool capable of handling sequence data from
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210 a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454, Ion Torrent
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211 and also PacBio).
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212
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213 It is particularly suited to small genomes such as bacteria.
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214
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215
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216 **Notes on paired reads**
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217
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218 .. class:: warningmark
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219
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220 MIRA uses read naming conventions to identify paired read partners
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221 (and does not care about their order in the input files). In most cases,
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222 the Solexa/Illumina setting is fine. For Sanger capillary sequencing,
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223 you may need to rename your reads to match one of the standard conventions
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224 supported by MIRA. For Roche 454 or Ion Torrent the appropriate settings
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225 depend on how the FASTQ file was produced:
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226
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227 * If using Roche's ``sffinfo`` or older versions of ``sff_extract``
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228 to convert SFF files to FASTQ, your reads will probably have the
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229 ``---> <---`` orientation and use the ``.f`` and ``.r``
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230 suffixes (FR naming).
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231
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232 * If using a recent version of ``sff_extract``, then the ``/1`` and ``/2``
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233 suffixes are used (Solexa/Illumina style naming) and the original
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234 ``2---> 1--->`` orientation is preserved.
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235
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236 The reason for this is the raw data for Roche 454 and Ion Torrent paired-end
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237 libraries sequences a circularised fragment such that the raw data begins
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238 with the end of the fragment, a linker, then the start of the fragment.
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239 This means both the start and end are sequenced from the same strand, and
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240 have the orientation ``2---> 1--->``. However, in order to use the data
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241 with traditional tools expecting Sanger capillary style ``---> <---``
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242 orientation it was common to reverse complement one of the pair to mimic this.
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243
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244
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245 **Citation**
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246
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247 If you use this Galaxy tool in work leading to a scientific publication please
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248 cite the following papers:
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249
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250 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
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251 Galaxy tools and workflows for sequence analysis with applications
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252 in molecular plant pathology. PeerJ 1:e167
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253 http://dx.doi.org/10.7717/peerj.167
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254
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255 Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999).
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256 Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
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257 Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
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258 http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html
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259
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260 This wrapper is available to install into other Galaxy Instances via the Galaxy
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261 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
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262 </help>
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263 </tool>
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