Mercurial > repos > peterjc > mira_assembler

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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira3/ commit 89578746a1c5b29c84a173d8b2709f086f69a7b6
author peterjc
date Mon, 03 Jun 2019 13:28:13 -0400
parents 2e7e2bc0d718
children
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83a94a5038a7 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira3/ commit fd979d17340cde155de176604744831d9597c6b6
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1 <tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.12">
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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="package" version="3.4.1.1">MIRA</requirement>
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5 </requirements>
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6 <version_command>
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7 python $__tool_directory__/mira.py -v
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8 </version_command>
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9 <command detect_errors="aggressive">
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10 python $__tool_directory__/mira.py mira '$out_fasta' '$out_qual' '$out_ace' '$out_caf' '$out_wig' '$out_log'
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11 ##Give the wrapper script list of output filenames, then the mira command...
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12 mira --job=$job_method,$job_type,$job_quality
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13
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14 ##Input files
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15 #if $condBackbone.use == "true":
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16 ## Can this be linked to job_method as well? If mapping we need the backbone...
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17 -SB:lb=1:bft=fasta -FN:bbin=${condBackbone.filename}
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18 #end if
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19 #if $condSanger.use == "true":
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20 SANGER_SETTINGS
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21 ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead
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22 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
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23 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename}
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24 #end if
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25 #if $condRoche.use == "true":
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26 454_SETTINGS
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27 ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead
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28 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
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29 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condRoche.filename}
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30 #end if
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31 #if $condIllumina.use == "true":
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32 SOLEXA_SETTINGS
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33 ## Not easy in Galaxy to add solexa to --job, so use load_sequence_data(lsd) instead
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34 -LR:lsd=1:ft=fastq -FN:fqi=${condIllumina.filename}
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35 ##TODO - Look at -LR FASTQ qual offset (fqqo)
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36 #end if
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37 #if $condIonTorrent.use == "true":
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38 IONTOR_SETTINGS
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39 ## Not easy in Galaxy to add iontor to --job, so use load_sequence_data(lsd) instead
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40 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
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41 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condIonTorrent.filename}
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42 #end if
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43
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44 ##Output files
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45 COMMON_SETTINGS
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46
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47 ##ignore warnings about long read names
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48 -MI:somrnl=0
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49
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50 ##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output
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51 ##Explicitly disable formats we won't use like MAF (reduce IO)
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52 -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0
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53
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54 ##remove_rollover_tmps, remove_tmp_directory
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55 -OUT:rrot=1:rtd=1
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56
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57 ##put mira temp directory on local storage
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58 -DI:trt=/tmp
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59
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60 </command>
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61 <inputs>
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62 <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)">
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63 <option value="denovo">De novo</option>
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64 <option value="mapping">Mapping</option>
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65 </param>
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66 <param name="job_type" type="select" label="Assembly type">
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67 <option value="genome">Genome</option>
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68 <option value="est">EST (transcriptome)</option>
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69 </param>
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70 <param name="job_quality" type="select" label="Assembly quality grade">
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71 <option value="accurate">Accurate</option>
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72 <option value="normal">Normal (deprecated)</option>
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73 <option value="draft">Draft</option>
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74 </param>
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75 <!-- Backbone -->
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76 <conditional name="condBackbone">
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77 <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly.">
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78 <option value="false">No</option>
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79 <option value="true">Yes</option>
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80 </param>
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81 <when value="false" />
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82 <when value="true">
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83 <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) -->
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84 <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" />
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85 </when>
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86 </conditional>
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87 <!-- Sanger -->
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88 <conditional name="condSanger">
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89 <param name="use" type="select" label="Sanger/Capillary reads?">
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90 <option value="false">No</option>
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91 <option value="true">Yes</option>
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92 </param>
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93 <when value="false" />
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94 <when value="true">
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95 <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" />
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96 </when>
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97 </conditional>
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98 <!-- Roche 454 -->
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99 <conditional name="condRoche">
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100 <param name="use" type="select" label="454 reads?">
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101 <option value="false">No</option>
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102 <option value="true">Yes</option>
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103 </param>
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104 <when value="false" />
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105 <when value="true">
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106 <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences -->
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107 <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" />
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108 </when>
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109 </conditional>
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110 <!-- Illumina -->
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111 <conditional name="condIllumina">
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112 <param name="use" type="select" label="Solexa/Illumina reads?">
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113 <option value="false">No</option>
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114 <option value="true">Yes</option>
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115 </param>
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116 <when value="false" />
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117 <when value="true">
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118 <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" />
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119 </when>
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120 </conditional>
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121 <!-- Ion Torrent -->
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122 <conditional name="condIonTorrent">
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123 <param name="use" type="select" label="Ion Torrent reads?">
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124 <option value="false">No</option>
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125 <option value="true">Yes</option>
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126 </param>
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127 <when value="false" />
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128 <when value="true">
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129 <!-- TODO? Support SFF files directly, e.g. with sff_extract -->
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130 <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" />
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131 </when>
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132 </conditional>
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133 </inputs>
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134 <outputs>
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135 <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" />
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136 <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" />
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137 <data name="out_caf" format="txt" label="MIRA contigs (CAF)" />
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138 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
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139 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
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140 <data name="out_log" format="txt" label="MIRA log" />
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141 </outputs>
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142 <tests>
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143 <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses
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144 strain data and miraSearchESTSNPs. Here we just assemble it. -->
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145 <test>
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146 <param name="job_method" value="denovo" />
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147 <param name="job_type" value="est" />
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148 <param name="job_qual" value="accurate" />
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149 <param name="condBackbone|use" value="false" />
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150 <param name="condSanger|use" value="true" />
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151 <param name="condSanger|filename" value="tvc_mini.fastq" ftype="fastq" />
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152 <param name="condRoche|use" value="false" />
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153 <param name="condIllumina|use" value="false" />
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154 <param name="condIonTorrent|use" value="false" />
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155 <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />
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156 <output name="out_qual" file="empty_file.dat" compare="contains" />
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157 <output name="out_caf" file="empty_file.dat" compare="contains" />
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158 <output name="out_ace" file="empty_file.dat" compare="contains" />
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159 <output name="out_wig" file="empty_file.dat" compare="contains" />
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160 <output name="out_log" file="empty_file.dat" compare="contains" />
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161 </test>
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162 </tests>
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163 <help>
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164
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165 **What it does**
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166
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167 Runs MIRA v3.4, collects the output, and throws away all the temporary files.
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168
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169 MIRA is an open source assembly tool capable of handling sequence data from
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170 a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454 and also
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171 Ion Torrent).
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172
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173 It is particularly suited to small genomes such as bacteria.
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174
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175 **Citation**
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176
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177 If you use this Galaxy tool in work leading to a scientific publication please
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178 cite the following papers:
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179
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180 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
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181 Galaxy tools and workflows for sequence analysis with applications
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182 in molecular plant pathology. PeerJ 1:e167
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183 https://doi.org/10.7717/peerj.167
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184
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185 Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999).
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186 Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
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187 Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
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188 http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html
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189
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190 This wrapper is available to install into other Galaxy Instances via the Galaxy
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191 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
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192
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193 </help>
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194 <citations>
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195 <citation type="doi">10.7717/peerj.167</citation>
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196 <citation type="bibtex">@ARTICLE{Chevreux1999-mira3,
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197 author = {B. Chevreux and T. Wetter and S. Suhai},
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198 year = {1999},
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199 title = {Genome Sequence Assembly Using Trace Signals and Additional Sequence Information},
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200 journal = {Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB)}
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201 volume = {99},
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202 pages = {45-56},
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203 url = {http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html}
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204 }</citation>
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205 </citations>
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206 </tool>