Mercurial > repos > iuc > berokka

annotate berokka.xml @ 1:f91f6054fca7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 0f23197bb8b21c1499d8afa6d22c071dfa296a0f"
author iuc
date Thu, 30 Sep 2021 13:58:36 +0000
parents 9a1626faa05c
children 18c0086450bb
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f91f6054fca7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 0f23197bb8b21c1499d8afa6d22c071dfa296a0f"
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1 <tool id="berokka" name="Berokka" version="@TOOL_VERSION@" profile="19.01">
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2 <description>Trim, circularise, orient and filter long read bacterial genome assemblies</description>
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f91f6054fca7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 0f23197bb8b21c1499d8afa6d22c071dfa296a0f"
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.2.3</token>
f91f6054fca7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 0f23197bb8b21c1499d8afa6d22c071dfa296a0f"
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5 </macros>
0
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">berokka</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 berokka
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11 --outdir default '${input_file}'
9a1626faa05c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
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12
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13 #if $filter_fasta:
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14 --filter '${filter_fasta}'
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15 #end if
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16
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17 --readlen '${read_length}'
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18
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19 --fuzz '${fuzz}'
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20
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21 #unless $anno:
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22 --noanno
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23 #end unless
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24
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25 ]]></command>
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26 <inputs>
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27 <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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28 <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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29 <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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30 <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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31 <param name="anno" type="boolean" checked="true" label="Annotation" help="Annotate Trimmed FASTA"/>
9a1626faa05c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
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32 </inputs>
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33 <outputs>
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34 <data name="trimmed" format="fasta" from_work_dir="default/02.trimmed.fa" label="${tool.name} on ${on_string}: Trimmed"/>
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35 <data name="results" format="tabular" from_work_dir="default/03.results.tab" label="${tool.name} on ${on_string}: Results"/>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="input_file" value="berokka_test1.fasta"/>
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40 <param name="read_length" value="60000"/>
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41 <param name="fuzz" value="5"/>
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42 <param name="anno" value="true"/>
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43 <output name="trimmed" file="trimmed_1" ftype="fasta"/>
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44 <output name="results" file="results_1" ftype="tabular"/>
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45 </test>
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46 <test>
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47 <param name="input_file" value="berokka_test1.fasta"/>
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48 <param name="filter_select" value="true"/>
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49 <param name="filter_fasta" value="berokka_test1.fasta"/>
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50 <param name="read_length" value="60000"/>
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51 <param name="fuzz" value="5"/>
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52 <param name="anno" value="true"/>
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53 <output name="trimmed" file="trimmed_2" ftype="fasta"/>
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54 <output name="results" file="results_2" ftype="tabular"/>
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55 </test>
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56 <test>
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57 <param name="input_file" value="berokka_test1.fasta"/>
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58 <param name="read_length" value="100"/>
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59 <param name="fuzz" value="50"/>
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60 <param name="anno" value="false"/>
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61 <output name="trimmed" file="trimmed_3" ftype="fasta"/>
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62 <output name="results" file="results_3" ftype="tabular"/>
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63 </test>
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64 </tests>
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65 <help><![CDATA[
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66 **Summary**
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67
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68 Trim, circularise, orient & filter long read bacterial genome assemblies
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69 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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70
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71 You should only try Berokka if:
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72
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73 1. You only have the contig files and do not have the corrected reads anymore
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74 2. Your contigs are simple cases with clear overhang and could be done manually with BLAST
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75 3. Circlator fails on your data even after troubleshooting
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76
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77 NOTE: orientation to dnaA or rep genes is not yet implemented.
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78
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79 **Input**
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80
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81 Input should be completed long-read assemblies in FASTA format, such as those from CANU or HGAP.
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82
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83 **Output**
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84
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85 1. trimmed: The (possibly) trimmed sequences (FASTA)
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86
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87 2. results: Summary of results (TSV)
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88
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89 **Options**
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90
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91 * `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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92
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93 * `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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94
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95 * `Fuzz` can be used to accept local alignment within X bp of global (default '5')
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96
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97 * `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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98
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99 ]]></help>
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100 <citations>
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101 <citation type="bibtex">
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102 @UNPUBLISHED{Seemann2016,
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103 author = {Seemann, Torsten},
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104 title = {Berokka: Faster Trim, circularise and orient long read bacterial genome assemblies},
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105 year = {2016},
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106 url = {https://github.com/tseemann/berokka},
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107 }
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108 </citation>
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109 </citations>
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110 </tool>