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1 <tool id="quast" name="Quast" version="1.0.0" >
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2 <description>QUAST (Quality ASsessment Tool) evaluates genome assemblies.</description>
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3
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4 <requirements>
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5 <requirement type="package" version="3.2">quast</requirement>
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6 </requirements>
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7
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8 <stdio>
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9 <exit_code range="1:" level="fatal" description="The tool's exit code was 1, which suggests that something went wrong." />
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10 </stdio>
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11
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12 <command>
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13 quast.py
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14 -o outputdir
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15
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16 #if $gene_selection == "eukaryote" :
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17 --eukaryote
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18 #end if
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19
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20 #if $gene_selection == "Metagenes" :
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21 --meta
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22 #end if
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23
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24 --min-contig $min_contig
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25
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26
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27 #for $i in $files:
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28 $i.input
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29 #end for
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30 ;
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31 cp outputdir/report.txt $quast_out;
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32 </command>
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33
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34 <inputs>
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35 <repeat name="files" title="Input contig files">
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36 <param type="data" format="fasta" name="input" label="Contigs output file"/>
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37 </repeat>
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38 <param name="gene_selection" type="select">
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39 <option value="prokaryotes">Prokaryotes</option>
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40 <option value="eukaryote">Eukaryote</option>
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41 <option value="metagenes">Metagenomes</option>
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42 </param>
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43 <param name="min_contig" type="integer" value="500" label="Set the threshold for the contig length (default is 500)"/>
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44 </inputs>
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45
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46 <outputs>
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47 <data format="txt" name="quast_out" label="Quast report.txt" from_work_dir="Quast_report.txt"/>
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48 </outputs>
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49
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50 <tests>
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51 <test>
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52 <param name="input" value="input_contigs_1.fasta"/>
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53 <param name="gene_selection" value="eukaryote"/>
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54 <param name="min_config" value="500"/>
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55 <output name="quast_out" file="output_Quast_report.txt"/>
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56 </test>
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57 </tests>
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58
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59 <help>
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60 **Description**
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61
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62 Galaxy tool wrapper for the QUAST tool. Quast stands for QUality ASsessment Tool. It evalutes genome assemblies by computing various metrics.
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63 For more information regarding the settings of the tool, please visit the QUAST 3.2 Manual on http://quast.bioinf.spbau.ru/manual.html
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64
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65 -----
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66
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67 **Inputs and Outputs**
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68
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69 - Input:
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70 + The tool accepts assemblies and references in FASTA format.
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71
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72 - Output:
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73 + An assessment summary in plain text format
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74
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75
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76 -----
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77
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78 **Tool Information**
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79
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80 - QUAST Tool v3.2:
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81 + Release Date: November 2015
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82 + URL: http://bioinf.spbau.ru/quast
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83 + Source URL: https://downloads.sourceforge.net/project/quast/quast-3.2.tar.gz
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84
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85 -----
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86
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87 **QUAST Galaxy Wrapper Author and Contact Information**
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88
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89 + Jacob Jablonski
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90 + AAFC-MBB Team
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91 + Email: mbb@agr.gc.ca
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92 + Agriculture and Agri-foods Canada, Ottawa, ON, Canada
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93
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94 </help>
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95
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96 <citations>
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97 <citation type="bibtex">@ARTICLE{a1,
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98 author = {Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler},
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99 title = {QUAST: quality assessment tool for genomce assemblies, Bioinformatics (2013) 29 (8): 1072-1075}
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100 }</citation>
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101 </citations>
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102 </tool>
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103
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