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annotate mira_wrapper_v0.0.2.tar.gz/tools/sr_assembly/mira.xml @ 1:e53a79816f5f

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v0.0.2 - Improve capture of stdout/stderr (should see it as it runs)
author peterjc
date Thu, 16 Jun 2011 04:44:00 -0400
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1 <tool id="mira_assembler" name="Assemble with MIRA" version="0.0.2">
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2 <description>Takes Sanger, Roche, and Illumina data</description>
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3 <command interpreter="python">mira.py mira $out_fasta $out_qual $out_tcs $out_ace $out_caf $out_wig $out_log
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4 ##Give the wrapper script list of output filenames, then the mira command...
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5 mira --job=$job_method,$job_type,$job_quality
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6
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7 ##Input files
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8 #if $condBackbone.use == "true":
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9 ## Can this be linked to job_method as well? If mapping we need the backbone...
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10 -SB:lb=yes -SB:bft=fasta -FN:bbin=${condBackbone.filename}
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11 #end if
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12 #if $condSanger.use == "true":
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13 Sanger_SETTINGS
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14 ## Not easy to add sanger to --job, so use load_sequence_data(lsd) instead
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15 -LR:lsd=yes
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16 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
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17 -LR:mxti=no -LR:ft=fastq -FN:fqi=${condSanger.filename}
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18 #end if
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19 #if $condRoche.use == "true":
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20 454_SETTINGS
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21 ## Not easy to add 454 to --job, so use load_sequence_data(lsd) instead
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22 -LR:lsd=yes
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23 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
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24 -LR:mxti=no -LR:ft=fastq -FN:fqi=${condRoche.filename}
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25 #end if
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26 #if $condIllumina.use == "true":
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27 SOLEXA_SETTINGS
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28 ## Not easy to add solexa to --job, so use load_sequence_data(lsd) instead
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29 -LR:lsd=yes -LR:ft=fastq -FN:fgi=${condIllumina.filename}
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30 ##TODO - Look at -LR FASTQ qual offset (fqqo)
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31 #end if
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32
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33
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34 ##Output files
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35 COMMON_SETTINGS
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36 ##remove_rollover_logs, remove_log_directory
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37 -OUT:rrol=yes -OUT:rld=yes
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38
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39 </command>
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40 <inputs>
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41 <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)">
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42 <option value="denovo">De novo</option>
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43 <option value="mapping">Mapping</option>
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44 </param>
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45 <param name="job_type" type="select" label="Assembly type">
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46 <option value="genome">Genome</option>
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47 <option value="est">EST (transcriptome)</option>
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48 </param>
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49 <param name="job_quality" type="select" label="Assembly quality grade">
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50 <option value="normal">Normal</option>
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51 <option value="draft">Draft</option>
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52 <option value="accurate">Accurate</option>
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53 </param>
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54 <!-- Backbone -->
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55 <conditional name="condBackbone">
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56 <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly.">
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57 <option value="false">No</option>
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58 <option value="true">Yes</option>
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59 </param>
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60 <when value="false" />
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61 <when value="true">
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62 <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) -->
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63 <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" />
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64 </when>
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65 </conditional>
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66 <!-- Sanger -->
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67 <conditional name="condSanger">
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68 <param name="use" type="select" label="Sanger/Capillary reads?">
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69 <option value="false">No</option>
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70 <option value="true">Yes</option>
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71 </param>
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72 <when value="false" />
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73 <when value="true">
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74 <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" />
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75 </when>
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76 </conditional>
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77 <!-- Roche 454 -->
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78 <conditional name="condRoche">
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79 <param name="use" type="select" label="454 reads?">
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80 <option value="false">No</option>
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81 <option value="true">Yes</option>
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82 </param>
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83 <when value="false" />
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84 <when value="true">
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85 <param name="filename" type="data" format="fastq,sff" label="Roche 454 reads file" help="FASTQ format" />
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86 </when>
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87 </conditional>
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88 <!-- Illumina -->
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89 <conditional name="condIllumina">
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90 <param name="use" type="select" label="Solexa/Illumina reads?">
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91 <option value="false">No</option>
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92 <option value="true">Yes</option>
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93 </param>
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94 <when value="false" />
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95 <when value="true">
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96 <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" />
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97 </when>
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98 </conditional>
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99 </inputs>
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100 <outputs>
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101 <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" />
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102 <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" />
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103 <data name="out_tcs" format="tabular" label="MIRA contigs summary" />
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104 <data name="out_caf" format="txt" label="MIRA contigs (CAF)" />
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105 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
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106 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
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107 <data name="out_log" format="txt" label="MIRA log" />
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108 </outputs>
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109 <tests>
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110 </tests>
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111 <requirements>
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112 <requirement type="python-module">Bio</requirement>
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113 </requirements>
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114 <help>
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115
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116 **What it does**
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117
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118 Runs MIRA v3, collects the output, and throws away all the temporary files.
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119
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120 The MIRA transposed contig summary (TCS) file is converted into a tabular file for use within Galaxy.
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121 This records one line per base per contig, and including things like the base, quality, coverage and any tags.
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122
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123 **Citation**
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124
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125 This tool uses MIRA. If you use this tool in scientific work leading to a
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126 publication, please cite:
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127
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128 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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129
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130 </help>
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131 </tool>