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1 <tool id="mira_assembler" name="Assemble with MIRA" version="0.0.6">
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2 <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
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3 <version_command interpreter="python">mira.py -v</version_command>
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4 <command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log
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5 ##Give the wrapper script list of output filenames, then the mira command...
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6 mira --job=$job_method,$job_type,$job_quality
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7
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8 ##Input files
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9 #if $condBackbone.use == "true":
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10 ## Can this be linked to job_method as well? If mapping we need the backbone...
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11 -SB:lb=1:bft=fasta -FN:bbin=${condBackbone.filename}
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12 #end if
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13 #if $condSanger.use == "true":
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14 SANGER_SETTINGS
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15 ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead
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16 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
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17 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename}
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18 #end if
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19 #if $condRoche.use == "true":
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20 454_SETTINGS
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21 ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead
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22 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
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23 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condRoche.filename}
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24 #end if
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25 #if $condIllumina.use == "true":
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26 SOLEXA_SETTINGS
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27 ## Not easy in Galaxy to add solexa to --job, so use load_sequence_data(lsd) instead
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28 -LR:lsd=1:ft=fastq -FN:fqi=${condIllumina.filename}
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29 ##TODO - Look at -LR FASTQ qual offset (fqqo)
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30 #end if
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31 #if $condIonTorrent.use == "true":
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32 IONTOR_SETTINGS
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33 ## Not easy in Galaxy to add iontor to --job, so use load_sequence_data(lsd) instead
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34 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
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35 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condIonTorrent.filename}
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36 #end if
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37
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38 ##Output files
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39 COMMON_SETTINGS
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40
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41 ##ignore warnings about long read names
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42 -MI:somrnl=0
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43
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44 ##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output
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45 ##Explicitly disable formats we won't use like MAF (reduce IO)
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46 -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0
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47
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48 ##remove_rollover_tmps, remove_tmp_directory
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49 -OUT:rrot=1:rtd=1
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50
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51 ##put mira temp directory on local storage
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52 -DI:trt=/tmp
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53
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54 </command>
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55 <inputs>
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56 <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)">
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57 <option value="denovo">De novo</option>
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58 <option value="mapping">Mapping</option>
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59 </param>
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60 <param name="job_type" type="select" label="Assembly type">
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61 <option value="genome">Genome</option>
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62 <option value="est">EST (transcriptome)</option>
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63 </param>
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64 <param name="job_quality" type="select" label="Assembly quality grade">
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65 <option value="accurate">Accurate</option>
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66 <option value="normal">Normal (deprecated)</option>
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67 <option value="draft">Draft</option>
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68 </param>
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69 <!-- Backbone -->
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70 <conditional name="condBackbone">
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71 <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly.">
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72 <option value="false">No</option>
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73 <option value="true">Yes</option>
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74 </param>
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75 <when value="false" />
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76 <when value="true">
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77 <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) -->
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78 <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" />
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79 </when>
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80 </conditional>
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81 <!-- Sanger -->
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82 <conditional name="condSanger">
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83 <param name="use" type="select" label="Sanger/Capillary reads?">
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84 <option value="false">No</option>
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85 <option value="true">Yes</option>
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86 </param>
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87 <when value="false" />
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88 <when value="true">
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89 <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" />
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90 </when>
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91 </conditional>
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92 <!-- Roche 454 -->
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93 <conditional name="condRoche">
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94 <param name="use" type="select" label="454 reads?">
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95 <option value="false">No</option>
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96 <option value="true">Yes</option>
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97 </param>
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98 <when value="false" />
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99 <when value="true">
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100 <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences -->
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101 <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" />
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102 </when>
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103 </conditional>
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104 <!-- Illumina -->
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105 <conditional name="condIllumina">
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106 <param name="use" type="select" label="Solexa/Illumina reads?">
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107 <option value="false">No</option>
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108 <option value="true">Yes</option>
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109 </param>
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110 <when value="false" />
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111 <when value="true">
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112 <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" />
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113 </when>
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114 </conditional>
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115 <!-- Ion Torrent -->
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116 <conditional name="condIonTorrent">
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117 <param name="use" type="select" label="Ion Torrent reads?">
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118 <option value="false">No</option>
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119 <option value="true">Yes</option>
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120 </param>
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121 <when value="false" />
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122 <when value="true">
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123 <!-- TODO? Support SFF files directly, e.g. with sff_extract -->
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124 <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" />
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125 </when>
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126 </conditional>
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127 </inputs>
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128 <outputs>
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129 <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" />
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130 <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" />
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131 <data name="out_caf" format="txt" label="MIRA contigs (CAF)" />
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132 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
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133 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
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134 <data name="out_log" format="txt" label="MIRA log" />
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135 </outputs>
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136 <tests>
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137 </tests>
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138 <requirements>
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139 <requirement type="python-module">Bio</requirement>
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140 <requirement type="binary">mira</requirement>
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141 </requirements>
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142 <help>
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143
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144 **What it does**
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145
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146 Runs MIRA v3.4, collects the output, and throws away all the temporary files.
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147
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148 **Citation**
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149
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150 If you use this tool in scientific work leading to a publication, please cite:
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151
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152 Chevreux et al. (1999) Genome Sequence Assembly Using Trace Signals and Additional Sequence Information Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
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153
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154 </help>
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155 </tool>
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