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annotate berokka.xml @ 0:9a1626faa05c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
author iuc
date Mon, 25 Mar 2019 12:55:16 -0400
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children f91f6054fca7
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9a1626faa05c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
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1 <tool id="berokka" name="Berokka" version="0.2">
9a1626faa05c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
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2 <description>Trim, circularise, orient and filter long read bacterial genome assemblies</description>
9a1626faa05c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
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3 <requirements>
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4 <requirement type="package" version="0.2">berokka</requirement>
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5 </requirements>
9a1626faa05c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
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6 <command detect_errors="exit_code"><![CDATA[
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7 berokka
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8 --outdir default '${input_file}'
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9
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10 #if $filter_fasta:
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11 --filter '${filter_fasta}'
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12 #end if
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14 --readlen '${read_length}'
9a1626faa05c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
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16 --fuzz '${fuzz}'
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17
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18 #unless $anno:
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19 --noanno
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20 #end unless
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21
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22 ]]></command>
9a1626faa05c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
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23 <inputs>
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24 <param name="input_file" type="data" format="fasta" label="Input (FASTA)" help="Should be completed long-read assemblies in FASTA format, such as those from CANU or HGAP"/>
9a1626faa05c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
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25 <param name="filter_fasta" optional="true" type="data" format="fasta" label="Filter (FASTA)" help="Give a fasta to use as a filter."/>
9a1626faa05c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
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26 <param name="read_length" type="integer" value="60000" min="28" label="Read Length" help="Approximate max read length (default '60000')"/>
9a1626faa05c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
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27 <param name="fuzz" type="integer" value="5" label="Fuzz" help="Accept local alignment within X bp of global (default '5')"/>
9a1626faa05c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
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28 <param name="anno" type="boolean" checked="true" label="Annotation" help="Annotate Trimmed FASTA"/>
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29 </inputs>
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30 <outputs>
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31 <data name="trimmed" format="fasta" from_work_dir="default/02.trimmed.fa" label="${tool.name} on ${on_string}: Trimmed"/>
9a1626faa05c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
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32 <data name="results" format="tabular" from_work_dir="default/03.results.tab" label="${tool.name} on ${on_string}: Results"/>
9a1626faa05c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="input_file" value="berokka_test1.fasta"/>
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37 <param name="read_length" value="60000"/>
9a1626faa05c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
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38 <param name="fuzz" value="5"/>
9a1626faa05c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
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39 <param name="anno" value="true"/>
9a1626faa05c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
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40 <output name="trimmed" file="trimmed_1" ftype="fasta"/>
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41 <output name="results" file="results_1" ftype="tabular"/>
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42 </test>
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43 <test>
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44 <param name="input_file" value="berokka_test1.fasta"/>
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45 <param name="filter_select" value="true"/>
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46 <param name="filter_fasta" value="berokka_test1.fasta"/>
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47 <param name="read_length" value="60000"/>
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48 <param name="fuzz" value="5"/>
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49 <param name="anno" value="true"/>
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50 <output name="trimmed" file="trimmed_2" ftype="fasta"/>
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51 <output name="results" file="results_2" ftype="tabular"/>
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52 </test>
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53 <test>
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54 <param name="input_file" value="berokka_test1.fasta"/>
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55 <param name="read_length" value="100"/>
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56 <param name="fuzz" value="50"/>
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57 <param name="anno" value="false"/>
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58 <output name="trimmed" file="trimmed_3" ftype="fasta"/>
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59 <output name="results" file="results_3" ftype="tabular"/>
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63 **Summary**
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64
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65 Trim, circularise, orient & filter long read bacterial genome assemblies
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66 There is already a good piece of software to trim/circularise and orient genome assemblies called Circlator. Please try that first!
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67
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68 You should only try Berokka if:
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69
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70 1. You only have the contig files and do not have the corrected reads anymore
9a1626faa05c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
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71 2. Your contigs are simple cases with clear overhang and could be done manually with BLAST
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72 3. Circlator fails on your data even after troubleshooting
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73
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74 NOTE: orientation to dnaA or rep genes is not yet implemented.
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75
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76 **Input**
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77
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78 Input should be completed long-read assemblies in FASTA format, such as those from CANU or HGAP.
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79
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80 **Output**
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81
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82 1. trimmed: The (possibly) trimmed sequences (FASTA)
9a1626faa05c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
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83
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84 2. results: Summary of results (TSV)
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85
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86 **Options**
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87
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88 * `Filter <FASTA>` allows you to remove contigs which match 50% of sequences in this file. Berokka comes with the standard Pacbio control sequence. You can provide your own FASTA file using this option.
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89
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90 * `Read Length <LENGTH>` can be used for datasets that won't seem to circularise. It affects the length of the match it attempts to make using BLAST.
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91
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92 * `Fuzz` can be used to accept local alignment within X bp of global (default '5')
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93
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94 * `Annotation` can be set to "No" to ensure that the FASTA descriptions are not altered between the input and output FASTA files.
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95
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96 ]]></help>
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97 <citations>
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98 <citation type="bibtex">
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99 @UNPUBLISHED{Seemann2016,
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100 author = {Seemann, Torsten},
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101 title = {Berokka: Faster Trim, circularise and orient long read bacterial genome assemblies},
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102 year = {2016},
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103 url = {https://github.com/tseemann/berokka},
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104 }
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105 </citation>
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106 </citations>
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107 </tool>