Mercurial > repos > peterjc > mira4_assembler

annotate tools/mira4/mira4_de_novo.xml @ 1:99fde64b9563 draft

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Uploaded v0.0.1 preview1, escape ampersand in XML
author peterjc
date Thu, 26 Sep 2013 12:25:21 -0400
parents 32f693f6e741
children df86ed992a1b
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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, Illumina, Ion Torrent and PacBio 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="4.0">MIRA</requirement>
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7 </requirements>
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8 <version_command interpreter="python">mira4.py -v</version_command>
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9 <command interpreter="python">
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10 mira4.py $manifest $out_maf $out_fasta $out_log
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11 </command>
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12 <inputs>
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13 <param name="job_type" type="select" label="Assembly type">
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14 <option value="genome">Genome</option>
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15 <option value="est">EST (transcriptome)</option>
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16 </param>
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17 <param name="job_quality" type="select" label="Assembly quality grade">
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18 <option value="accurate">Accurate</option>
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19 <option value="draft">Draft</option>
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20 </param>
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21 <repeat name="read_group" title="Read Group" min="1">
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22 <param name="technology" type="select" label="Read technology" help="MIRA has different error models for different technologies">
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23 <option value="solexa">Solexa/Illumina</option>
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24 <option value="sanger">Sanger cappillary sequencing</option>
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25 <option value="454">Roche 454</option>
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26 <option value="iontor">Ion Torrent</option>
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27 <option value="pcbiolq">PacBio low quality (raw)</option>
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28 <option value="pcbiohq">PacBio high quality (corrected)</option>
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29 <option value="text">Synthetic reads (database entries, consensus sequences, artifical reads, etc)</option>
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30 <!-- TODO reference/backbone as an entry here? -->
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31 </param>
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32 <repeat name="reads" title="Reads" min="1" help="Paired reads can be combined into one file, or given as two files. MIRA will look at the read names to identify pairs.">
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33 <param name="filename" type="data" format="fastq" label="Reads in FASTQ format" />
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34 </repeat>
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35 </repeat>
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36 </inputs>
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37 <outputs>
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38 <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" />
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39 <data name="out_maf" format="mira" label="MIRA Assembly" />
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40 <data name="out_log" format="txt" label="MIRA log" />
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41 </outputs>
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42 <configfiles>
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43 <configfile name="manifest">
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44 project = MIRA
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45 job = denovo,${job_type},${job_quality}
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46 parameters = -GE:not=1 -NW:cmrnl -DI:trt=/tmp
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47 ## -GE:not is short for -GENERAL:number_of_threads and using one (1)
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48 ## can be useful for repeatability of assemblies and bug hunting.
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49 ##
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50 ## -NW:cmrnl is short for -NAG_AND_WARN:check_maxreadnamelength
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51 ## and without this MIRA aborts with read names over 40 characters
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52 ## due to limitations of some downstream tools.
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53 ##
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54 ## -DI:trt is short for -DIRECTORY:tmp_redirected_to and should
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55 ## point to a local hard drive (not something like NFS on network).
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56
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57 #for $rg in $read_group
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58 #=======================================================
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59 readgroup
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60 technology = ${rg.technology}
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61 ##MIRA will accept multiple filenames on one data line, or multiple data lines
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62 #for f in $rg.reads
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63 data = ${f.filename}
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64 #end for
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65 ### Cheetah doesn't want dollar sign on list comprehension intermediate variables
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66 ###set $files = ' '.join([str(f['filename']) for f in rg['reads']])
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67 ##data = $files
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68 #end for
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69 </configfile>
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70 </configfiles>
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71 <tests>
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72 <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses
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73 strain data and miraSearchESTSNPs. Here we just assemble it. -->
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74 <!--
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75 Commenting out test until Galaxy framework is fixed,
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76 https://trello.com/c/zSTrfDOB/820-disambiguated-conditional-parameters-not-supported-in-unit-tests
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77 <test>
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78 <param name="job_method" value="denovo" />
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79 <param name="job_type" value="est" />
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80 <param name="job_qual" value="accurate" />
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81 <param name="condBackbone.use" value="false" />
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82 <param name="condSanger.use" value="true" />
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83 <param name="condSanger.filename" value="tvc_mini.fastq" ftype="fastq" />
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84 <param name="condRoche.use" value="false" />
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85 <param name="condIllumina.use" value="false" />
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86 <param name="condIonTorrent.use" value="false" />
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87 <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />
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88 </test>
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89 -->
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90 </tests>
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91 <help>
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92
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93 **What it does**
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94
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95 Runs MIRA v4.0 in de novo mode, collects the output, and throws away all the temporary files.
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96
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97 MIRA is an open source assembly tool capable of handling sequence data from
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98 a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454, Ion Torrent
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99 and also PacBio).
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100
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101 It is particularly suited to small genomes such as bacteria.
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102
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103 **Citation**
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104
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105 If you use this Galaxy tool in work leading to a scientific publication please
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106 cite the following papers:
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107
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108 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
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109 Galaxy tools and workflows for sequence analysis with applications
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110 in molecular plant pathology. PeerJ 1:e167
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111 http://dx.doi.org/10.7717/peerj.167
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112
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113 Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999).
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114 Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
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115 Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
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116 http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html
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117
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118 This wrapper is available to install into other Galaxy Instances via the Galaxy
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119 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
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120 </help>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
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121 </tool>