Mercurial > repos > peterjc > mira_assembler

annotate tools/mira_3_4/mira.xml @ 6:1e49ca6731cd draft

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Uploaded v0.0.7 take 4, declare package dependency in main tool XML.
author peterjc
date Wed, 24 Apr 2013 12:54:44 -0400
parents c1c7d6f726b0
children e810e45bdad7
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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 <requirements>
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4 <requirement type="python-module">Bio</requirement>
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5 <requirement type="binary">mira</requirement>
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6 <requirement type="package" version="3.4.1.1">MIRA</requirement>
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7 </requirements>
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8 <version_command interpreter="python">mira.py -v</version_command>
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9 <command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log
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10 ##Give the wrapper script list of output filenames, then the mira command...
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11 mira --job=$job_method,$job_type,$job_quality
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12
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13 ##Input files
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14 #if $condBackbone.use == "true":
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15 ## Can this be linked to job_method as well? If mapping we need the backbone...
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16 -SB:lb=1:bft=fasta -FN:bbin=${condBackbone.filename}
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17 #end if
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18 #if $condSanger.use == "true":
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19 SANGER_SETTINGS
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20 ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead
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21 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
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22 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename}
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23 #end if
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24 #if $condRoche.use == "true":
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25 454_SETTINGS
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26 ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead
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27 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
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28 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condRoche.filename}
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29 #end if
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30 #if $condIllumina.use == "true":
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31 SOLEXA_SETTINGS
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32 ## Not easy in Galaxy to add solexa to --job, so use load_sequence_data(lsd) instead
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33 -LR:lsd=1:ft=fastq -FN:fqi=${condIllumina.filename}
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34 ##TODO - Look at -LR FASTQ qual offset (fqqo)
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35 #end if
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36 #if $condIonTorrent.use == "true":
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37 IONTOR_SETTINGS
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38 ## Not easy in Galaxy to add iontor to --job, so use load_sequence_data(lsd) instead
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39 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
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40 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condIonTorrent.filename}
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41 #end if
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42
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43 ##Output files
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44 COMMON_SETTINGS
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45
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46 ##ignore warnings about long read names
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47 -MI:somrnl=0
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48
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49 ##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output
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50 ##Explicitly disable formats we won't use like MAF (reduce IO)
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51 -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0
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52
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53 ##remove_rollover_tmps, remove_tmp_directory
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54 -OUT:rrot=1:rtd=1
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55
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56 ##put mira temp directory on local storage
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57 -DI:trt=/tmp
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58
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59 </command>
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60 <inputs>
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61 <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)">
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62 <option value="denovo">De novo</option>
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63 <option value="mapping">Mapping</option>
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64 </param>
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65 <param name="job_type" type="select" label="Assembly type">
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66 <option value="genome">Genome</option>
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67 <option value="est">EST (transcriptome)</option>
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68 </param>
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69 <param name="job_quality" type="select" label="Assembly quality grade">
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70 <option value="accurate">Accurate</option>
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71 <option value="normal">Normal (deprecated)</option>
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72 <option value="draft">Draft</option>
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73 </param>
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74 <!-- Backbone -->
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75 <conditional name="condBackbone">
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76 <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly.">
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77 <option value="false">No</option>
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78 <option value="true">Yes</option>
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79 </param>
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80 <when value="false" />
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81 <when value="true">
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82 <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) -->
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83 <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" />
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84 </when>
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85 </conditional>
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86 <!-- Sanger -->
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87 <conditional name="condSanger">
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88 <param name="use" type="select" label="Sanger/Capillary reads?">
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89 <option value="false">No</option>
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90 <option value="true">Yes</option>
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91 </param>
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92 <when value="false" />
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93 <when value="true">
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94 <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" />
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95 </when>
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96 </conditional>
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97 <!-- Roche 454 -->
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98 <conditional name="condRoche">
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99 <param name="use" type="select" label="454 reads?">
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100 <option value="false">No</option>
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101 <option value="true">Yes</option>
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102 </param>
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103 <when value="false" />
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104 <when value="true">
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105 <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences -->
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106 <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" />
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107 </when>
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108 </conditional>
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109 <!-- Illumina -->
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110 <conditional name="condIllumina">
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111 <param name="use" type="select" label="Solexa/Illumina reads?">
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112 <option value="false">No</option>
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113 <option value="true">Yes</option>
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114 </param>
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115 <when value="false" />
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116 <when value="true">
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117 <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" />
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118 </when>
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119 </conditional>
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120 <!-- Ion Torrent -->
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121 <conditional name="condIonTorrent">
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122 <param name="use" type="select" label="Ion Torrent reads?">
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123 <option value="false">No</option>
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124 <option value="true">Yes</option>
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125 </param>
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126 <when value="false" />
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127 <when value="true">
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128 <!-- TODO? Support SFF files directly, e.g. with sff_extract -->
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129 <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" />
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130 </when>
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131 </conditional>
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132 </inputs>
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133 <outputs>
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134 <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" />
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135 <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" />
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136 <data name="out_caf" format="txt" label="MIRA contigs (CAF)" />
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137 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
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138 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
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139 <data name="out_log" format="txt" label="MIRA log" />
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140 </outputs>
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141 <tests>
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142 </tests>
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143 <help>
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144
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145 **What it does**
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146
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147 Runs MIRA v3.4, collects the output, and throws away all the temporary files.
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148
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149 **Citation**
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150
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151 If you use this tool in scientific work leading to a publication, please cite:
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152
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153 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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154
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155 </help>
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156 </tool>