Mercurial > repos > peterjc > mira4_assembler

annotate tools/mira4/mira4_de_novo.xml @ 7:902f01c1084b draft

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Uploaded v0.0.1 preview 7, with mirabait wrapper
author peterjc
date Fri, 25 Oct 2013 07:18:38 -0400
parents 626d5cfd01aa
children 302d13490b23
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1 <tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.1">
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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="package" version="4.0">MIRA</requirement>
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6 </requirements>
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7 <version_command interpreter="python">mira4.py --version</version_command>
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8 <command interpreter="python">
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9 mira4.py $manifest $out_maf $out_fasta $out_log
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10 </command>
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11 <inputs>
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12 <param name="job_type" type="select" label="Assembly type">
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13 <option value="genome">Genome</option>
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14 <option value="est">EST (transcriptome)</option>
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15 </param>
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16 <param name="job_quality" type="select" label="Assembly quality grade">
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17 <option value="accurate">Accurate</option>
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18 <option value="draft">Draft</option>
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19 </param>
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20 <repeat name="read_group" title="Read Group" min="1">
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21 <param name="technology" type="select" label="Read technology">
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22 <option value="solexa">Solexa/Illumina</option>
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23 <option value="sanger">Sanger cappillary sequencing</option>
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24 <option value="454">Roche 454</option>
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25 <option value="iontor">Ion Torrent</option>
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26 <option value="pcbiolq">PacBio low quality (raw)</option>
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27 <option value="pcbiohq">PacBio high quality (corrected)</option>
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28 <option value="text">Synthetic reads (database entries, consensus sequences, artifical reads, etc)</option>
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29 <!-- TODO reference/backbone as an entry here? -->
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30 </param>
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31 <conditional name="segments">
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32 <param name="type" type="select" label="Are these paired reads?">
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33 <option value="paired">Paired reads</option>
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34 <option value="none">Single reads or not relevant (e.g. primer walking with Sanger capillary sequencing)</option>
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35 </param>
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36 <when value="paired">
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37 <param name="placement" type="select" label="Pairing type (segment placing)">
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38 <option value="FR">---&gt; &lt;--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option>
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39 <option value="RF">&lt;--- ---&gt; (e.g. Solexa/Illumina mate-pair library)</option>
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40 <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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41 </param>
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42 <!-- min/max validation is done via the <code> tag -->
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43 <param name="min_size" type="integer" optional="true" min="0" value=""
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44 label="Minimum size of 'good' DNA templates in the library preparation"
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45 help="Optional, but if used you must also supply a maximum value." />
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46 <param name="max_size" type="integer" optional="true" min="0" value=""
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47 label="Maximum size of 'good' DNA templates in the library preparation"
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48 help="Optional, but if used you must also supply a minimum value." />
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49 <param name="naming" type="select" label="Pair naming convention">
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50 <option value="solexa">Solexa/Illumina (using '/1' and '/2' suffixes, or later Illumina colon system)</option>
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51 <option value="FR">Forward/Reverse scheme (using '.f*' and '.r*' suffixes)</option>
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52 <option value="tigr">TIGR scheme (using 'TF*' and 'TR*' suffixes)</option>
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53 <option value="sanger">Sanger scheme (see notes)</option>
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54 <option value="stlouis">St. Louis scheme (see notes)</option>
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55 </param>
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56 </when>
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57 <when value="none" /><!-- no further questions -->
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58 </conditional>
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59 <param name="filenames" type="data" format="fastq,mira" multiple="true" required="true" label="Read file(s)"
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60 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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61 </repeat>
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62 </inputs>
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63 <code file="mira4_validator.py" />
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64 <outputs>
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65 <data name="out_fasta" format="fasta" label="MIRA de novo contigs (FASTA)" />
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66 <data name="out_maf" format="mira" label="MIRA de novo assembly" />
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67 <data name="out_log" format="txt" label="MIRA de novo log" />
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68 </outputs>
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69 <configfiles>
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70 <configfile name="manifest">
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71 project = MIRA
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72 job = denovo,${job_type},${job_quality}
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73 parameters = -GE:not=1 -NW:cmrnl -DI:trt=/tmp
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74 ## -GE:not is short for -GENERAL:number_of_threads and using one (1)
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75 ## can be useful for repeatability of assemblies and bug hunting.
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76 ##
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77 ## -NW:cmrnl is short for -NAG_AND_WARN:check_maxreadnamelength
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78 ## and without this MIRA aborts with read names over 40 characters
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79 ## due to limitations of some downstream tools.
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80 ##
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81 ## -DI:trt is short for -DIRECTORY:tmp_redirected_to and should
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82 ## point to a local hard drive (not something like NFS on network).
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83
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84 #for $rg in $read_group
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85
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86 ##This bar goes into the manifest as a comment line
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87 #------------------------------------------------------------------------------
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88
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89 readgroup
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90 technology = ${rg.technology}
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91 ##Record the segment placement (if any)
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92 #if str($rg.segments.type) == "paired"
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93 segmentplacement = ${rg.segments.placement}
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94 segmentnaming = ${rg.segments.naming}
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95 #if str($rg.segments.min_size) != "" or str($rg.segments.max_size) != ""
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96 ##If our min/max validation failed I trust MIRA to give an error message...
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97 templatesize = $rg.segments.min_size $rg.segments.max_size
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98 #end if
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99 #end if
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100 #if str($rg.segments.type) == "none"
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101 segmentplacement = ?
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102 #end if
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103 ##MIRA will accept multiple filenames on one data line, or multiple data lines
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104 #for $f in $rg.filenames
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105 ##Must now map Galaxy datatypes to MIRA file types...
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106 #if $f.ext.startswith("fastq")
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107 ##MIRA doesn't like fastqsanger etc, just plain old fastq:
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108 data = fastq::$f
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109 #elif $f.ext == "mira"
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110 ##We're calling *.maf the "mira" format in Galaxy (name space collision)
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111 data = maf::$f
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112 #else
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113 ##MIRA is happy with fasta as name,
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114 data = ${f.ext}::$f
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115 #end if
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116 #end for
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117 #end for
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118 </configfile>
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119 </configfiles>
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120 <tests>
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121 <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses
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122 strain data and miraSearchESTSNPs. Here we just assemble it. -->
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123 <!--
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124 Commenting out test until Galaxy framework is fixed,
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125 https://trello.com/c/zSTrfDOB/820-disambiguated-conditional-parameters-not-supported-in-unit-tests
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126 <test>
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127 <param name="job_method" value="denovo" />
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128 <param name="job_type" value="est" />
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129 <param name="job_qual" value="accurate" />
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130 <param name="condBackbone.use" value="false" />
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131 <param name="condSanger.use" value="true" />
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132 <param name="condSanger.filename" value="tvc_mini.fastq" ftype="fastq" />
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133 <param name="condRoche.use" value="false" />
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134 <param name="condIllumina.use" value="false" />
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135 <param name="condIonTorrent.use" value="false" />
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136 <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />
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137 </test>
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138 -->
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139 </tests>
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140 <help>
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141
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142 **What it does**
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143
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144 Runs MIRA v4.0 in de novo mode, collects the output, and throws away all the temporary files.
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145
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146 MIRA is an open source assembly tool capable of handling sequence data from
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147 a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454, Ion Torrent
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148 and also PacBio).
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149
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150 It is particularly suited to small genomes such as bacteria.
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151
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152
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153 **Notes on paired reads**
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154
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155 .. class:: warningmark
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156
6
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157 MIRA uses read naming conventions to identify paired read partners
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158 (and does not care about their order in the input files). In most cases,
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159 the Solexa/Illumina setting is fine. For Sanger capillary sequencing,
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160 you may need to rename your reads to match one of the standard conventions
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161 supported by MIRA. For Roche 454 or Ion Torrent the appropriate settings
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162 depend on how the FASTQ file was produced:
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163
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164 * If using Roche's ``sffinfo`` or older versions of ``sff_extract``
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165 to convert SFF files to FASTQ, your reads will probably have the
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166 ``---&gt; &lt;---`` orientation and use the ``.f`` and ``.r``
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167 suffixes (FR naming).
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168
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169 * If using a recent version of ``sff_extract``, then the ``/1`` and ``/2``
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170 suffixes are used (Solexa/Illumina style naming) and the original
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171 ``2---&gt; 1---&gt;`` orientation is preserved.
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172
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173 The reason for this is the raw data for Roche 454 and Ion Torrent paired-end
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174 libraries sequences a circularised fragment such that the raw data begins
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175 with the end of the fragment, a linker, then the start of the fragment.
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176 This means both the start and end are sequenced from the same strand, and
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177 have the orientation ``2---&gt; 1---&gt;``. However, in order to use the data
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178 with traditional tools expecting Sanger capillary style ``---&gt; &lt;---``
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179 orientation it was common to reverse complement one of the pair to mimic this.
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180
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181
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182 **Citation**
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183
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184 If you use this Galaxy tool in work leading to a scientific publication please
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185 cite the following papers:
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186
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187 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
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188 Galaxy tools and workflows for sequence analysis with applications
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189 in molecular plant pathology. PeerJ 1:e167
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190 http://dx.doi.org/10.7717/peerj.167
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191
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192 Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999).
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193 Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
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194 Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
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195 http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html
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196
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197 This wrapper is available to install into other Galaxy Instances via the Galaxy
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198 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
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199 </help>
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200 </tool>