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annotate bakta.xml @ 6:92eee5f31117 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit fe9aabe924f278694d20b82169edacdb3e91eb49
author iuc
date Sun, 11 Feb 2024 00:56:12 +0000
parents 728dacaf08a9
children ba6990f72184
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iuc
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1 <tool id="bakta" name="Bakta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>
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3 Genome annotation via alignment-free sequence identification
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4 </description>
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5 <macros>
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6 <import>macro.xml</import>
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7 </macros>
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8 <expand macro='edam'/>
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9 <expand macro='xrefs'/>
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10 <expand macro="requirements"/>
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11 <expand macro="version_command"/>
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12
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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13 <command detect_errors="aggressive"><![CDATA[
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14
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15 mkdir -p ./database_path/amrfinderplus-db &&
865ece5ca178 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
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16 ln -s '$(input_option.bakta_db_select.fields.path)'/* database_path &&
865ece5ca178 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
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17 ln -s '$(input_option.amrfinder_db_select.fields.path)/' database_path/amrfinderplus-db/latest &&
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18 bakta --verbose
3f0aa1b3e816 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
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19
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20 #*======================================
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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21 CPU option
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22 ======================================*#
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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23 --threads \${GALAXY_SLOTS:-1}
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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24 #*======================================
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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25 Bakta database
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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26 ======================================*#
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27 --db './database_path'
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28 --output 'bakta_output'
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29 #if $input_option.min_contig_length
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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30 --min-contig-length $input_option.min_contig_length
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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31 #else if $annotation.compliant
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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32 --min-contig-length 200
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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33 #else
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34 --min-contig-length 1
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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35 #end if
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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36 --prefix bakta_output
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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37 #*======================================
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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38 Organism options
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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39 genus/species/strain/plasmid
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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40 ======================================*#
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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41 #if $organism.genus
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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42 --genus '$organism.genus'
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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43 #end if
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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44 #if $organism.species
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45 --species '$organism.species'
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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46 #end if
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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47 #if $organism.strain
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48 --strain '$organism.strain'
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49 #end if
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50 #if $organism.plasmid
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51 --plasmid '$organism.plasmid'
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52 #end if
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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53 #*======================================
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54 Annotation options
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55 gram type, prodigal/protein file
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56 ======================================*#
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57 $annotation.complete
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58 #if $annotation.prodigal
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59 --prodigal-tf '$annotation.prodigal'
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60 #end if
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61 #if $annotation.translation_table
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62 --translation-table '$annotation.translation_table'
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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63 #end if
3
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64 --gram '?'
0
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65 $annotation.keep_contig_headers
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66 #if $annotation.replicons
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67 --replicons '$annotation.replicons'
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68 #end if
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69 $annotation.compliant
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70 #if $annotation.proteins
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71 --proteins '$annotation.proteins'
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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72 #end if
6
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73 #if $annotation.regions
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74 --regions '$annotation.regions'
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75 #end if
0
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76 #*======================================
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77 Workflow OPTIONS
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78 skip some step of the bakta analysis
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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79 ======================================*#
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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80
2
debdc1469b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
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81 #echo " ".join($workflow.skip_analysis)
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1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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82
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83 #*======================================
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84 Genome file
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85 ======================================*#
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86 '$input_option.input_file'
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87 #*======================================
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88 LOG file
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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89 ======================================*#
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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90 | tee '$logfile'
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91 ]]></command>
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92 <inputs>
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93 <!-- DB and file INPUT -->
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94 <section name="input_option" title="Input/Output options" expanded="true">
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95 <param name="bakta_db_select" type="select" label="The bakta database">
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96 <options from_data_table="bakta_database">
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97 <filter type="static_value" value="@COMPATIBLE_BAKTA_VERSION@" column="bakta_version"/>
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98 <validator message="No bakta database is available" type="no_options"/>
0
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99 </options>
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100 </param>
2
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101 <param name="amrfinder_db_select" type="select" label="The amrfinderplus database">
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102 <options from_data_table="amrfinderplus_database">
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103 <validator message="No amrfinderplus database is available" type="no_options"/>
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104 </options>
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105 </param>
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106
0
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107 <param name="input_file" type="data" format="fasta,fasta.gz" label="Select genome in fasta format"/>
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108 <param name="min_contig_length" type="integer" optional="true" min="0" label="Minimum contig size" help="Minimum contig size (default = 1; 200 in compliant mode) (--min-contig-length)"/>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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109 </section>
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110 <!-- Organism INFORMATION OPTIONS -->
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111 <section name="organism" title="Optional organism options" expanded="false">
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112 <param argument="--genus" type="text" optional="true" label="Specify genus name" help="ex. Escherichia">
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113 <validator type="regex">^[a-zA-Z]+$</validator>
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114 </param>
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115 <param argument="--species" type="text" optional="true" label="Specify species name" help="ex. 'coli O157:H7'">
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116 <validator type="regex">^[a-zA-Z0-9\s(:\-/)]+$</validator>
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117 </param>
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118 <param argument="--strain" type="text" optional="true" label="Specify strain name" help="ex. Sakai">
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119 <validator type="regex">^[a-zA-Z]+$</validator>
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120 </param>
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121 <param argument="--plasmid" type="text" optional="true" label="Specify plasmid name" help="ex. pOSAK1">
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122 <validator type="regex">^[a-zA-Z0-9\s(:\-/)]+$</validator>
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123 </param>
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124 </section>
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125 <!-- ANNOTATION -->
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126 <section name="annotation" title="Optional annotation">
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127 <param argument="--complete" type="boolean" truevalue="--complete" falsevalue="" label="Complete replicons" help="All sequences are complete replicons (chromosome/plasmid[s])"/>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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128 <param argument="--prodigal" type="data" format="txt" optional="true" label="Prodigal file" help="Prodigal training file for CDS prediction"/>
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129 <param name="translation_table" type="select" optional="true" label="Translation table" help="Default is the bacterial table 11">
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130 <option value="4">4 Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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131 <option value="11" selected="true">11 Bacterial, Archaeal and Plant Plastid Code</option>
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132 </param>
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133 <param name="keep_contig_headers" type="boolean" truevalue="--keep-contig-headers" falsevalue="" label="Keep original contig header (--keep-contig-headers)"/>
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134 <param argument="--replicons" type="data" format="tabular,csv" optional="true" label="Replicon information table (tsv/csv)" help=""/>
0
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135 <param argument="--compliant" type="boolean" truevalue="--compliant" falsevalue="" label="Force Genbank/ENA/DDJB compliance"/>
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136 <param argument="--proteins" type="data" format="fasta" optional="true" label="Protein fasta file" help="Fasta file of trusted protein sequences for CDS annotation"/>
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137 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" label="Metagenome mode" help="Run in metagenome mode. This only affects CDS prediction"/>
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138 <param argument="--regions" type="data" format="gff,genbank" optional="true" label="Pre-annotated regions" help="Regions only, no functional annotations."/>
0
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139 </section>
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140 <!-- PARAMETER FOR WORKFLOW ANALYSIS -->
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141 <section name="workflow" title="Workflow option to skip steps">
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142 <param name="skip_analysis" type="select" display="checkboxes" multiple="true" label="Select steps to skip">
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143 <option value="--skip-trna">Skip tRNA detection and annotation</option>
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144 <option value="--skip-tmrna">Skip tmRNA detection and annotation</option>
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145 <option value="--skip-rrna">Skip rRNA detection and annotation</option>
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146 <option value="--skip-ncrna">Skip ncRNA detection and annotation</option>
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147 <option value="--skip-ncrna-region">Skip ncRNA region detection and annotation</option>
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148 <option value="--skip-crispr">Skip CRISPR array detection and annotation</option>
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149 <option value="--skip-cds">Skip CDS detection and annotation</option>
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150 <option value="--skip-pseudo">Skip pseudogene detection and annotation</option>
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151 <option value="--skip-sorf">Skip sORF detection and annotation</option>
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152 <option value="--skip-gap">Skip gap detection and annotation</option>
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153 <option value="--skip-ori">Skip oriC/oriT detection and annotation</option>
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154 <option value="--skip-plot">Skip generation of circular genome plots</option>
0
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155 </param>
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156 </section>
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157 <section name="output_files" title="Selection of the output files">
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158 <param name="output_selection" type="select" display="checkboxes" multiple="true" label="Output files selection">
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159 <option value="file_tsv" selected="true">Annotation file in TSV</option>
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160 <option value="file_gff3" selected="true">Annotation and sequence in GFF3</option>
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161 <option value="file_gbff" selected="false">Annotations and sequences in GenBank format</option>
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162 <option value="file_embl" selected="false">Annotations and sequences in EMBL format</option>
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163 <option value="file_fna" selected="false">Replicon/contig DNA sequences as FASTA</option>
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164 <option value="file_ffn" selected="true">Feature nucleotide sequences as FASTA</option>
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165 <option value="file_faa" selected="false">CDS/sORF amino acid sequences as FASTA</option>
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166 <option value="hypo_tsv" selected="false">Hypothetical protein CDS in TSV</option>
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167 <option value="hypo_fa" selected="false">Hypothetical protein CDS amino sequences as FASTA</option>
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168 <option value="sum_txt" selected="false">Summary as TXT</option>
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169 <option value="file_json" selected="false">Information on each annotated feature as JSON</option>
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170 <option value="file_plot" selected="true">Plot of the annotation result as SVG</option>
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171 <option value="log_txt" selected="false">Log file as TXT</option>
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172 </param>
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173 </section>
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174
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175 </inputs>
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176 <outputs>
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177 <data name="annotation_tsv" format="tabular" from_work_dir="bakta_output/bakta_output.tsv" label="${tool.name} on ${on_string}: annotation_summary">
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178 <filter>output_files['output_selection'] and "file_tsv" in output_files['output_selection']</filter>
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179 </data>
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180 <data name="annotation_gff3" format="gff3" from_work_dir="bakta_output/bakta_output.gff3" label="${tool.name} on ${on_string}: Annotation_and_sequences">
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181 <filter>output_files['output_selection'] and "file_gff3" in output_files['output_selection']</filter>
0
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182 </data>
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183 <data name="annotation_gbff" format="tabular" from_work_dir="bakta_output/bakta_output.gbff" label="${tool.name} on ${on_string}: bakta_output.gbff">
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184 <filter>output_files['output_selection'] and "file_gbff" in output_files['output_selection']</filter>
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185 </data>
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186 <data name="annotation_embl" format="tabular" from_work_dir="bakta_output/bakta_output.embl" label="${tool.name} on ${on_string}: bakta_output.embl">
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187 <filter>output_files['output_selection'] and "file_embl" in output_files['output_selection']</filter>
0
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188 </data>
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189 <data name="annotation_fna" format="fasta" from_work_dir="bakta_output/bakta_output.fna" label="${tool.name} on ${on_string}: Contig_sequences">
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190 <filter>output_files['output_selection'] and "file_fna" in output_files['output_selection']</filter>
0
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191 </data>
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192 <data name="annotation_ffn" format="fasta" from_work_dir="bakta_output/bakta_output.ffn" label="${tool.name} on ${on_string}: Nucleotide_sequences">
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193 <filter>output_files['output_selection'] and "file_ffn" in output_files['output_selection']</filter>
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194 </data>
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195 <data name="annotation_faa" format="fasta" from_work_dir="bakta_output/bakta_output.faa" label="${tool.name} on ${on_string}: Amino_acid_sequences">
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196 <filter>output_files['output_selection'] and "file_faa" in output_files['output_selection']</filter>
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197 </data>
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198 <data name="hypotheticals_tsv" format="tabular" from_work_dir="bakta_output/bakta_output.hypotheticals.tsv" label="${tool.name} on ${on_string}: hypothetical_annotation_summary">
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199 <filter>output_files['output_selection'] and "hypo_tsv" in output_files['output_selection']</filter>
0
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200 </data>
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201 <data name="hypotheticals_faa" format="fasta" from_work_dir="bakta_output/bakta_output.hypotheticals.faa" label="${tool.name} on ${on_string}: hypothetical_amino_acid_sequences">
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202 <filter>output_files['output_selection'] and "hypo_fa" in output_files['output_selection']</filter>
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203 </data>
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204 <data name="summary_txt" format="txt" from_work_dir="bakta_output/bakta_output.txt" label="${tool.name} on ${on_string}: Analysis_summary">
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205 <filter>output_files['output_selection'] and "sum_txt" in output_files['output_selection']</filter>
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206 </data>
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207 <data name="annotation_json" format="json" from_work_dir="bakta_output/bakta_output.json" label="${tool.name} on ${on_string}: annotation_machine_readable">
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208 <filter>output_files['output_selection'] and "file_json" in output_files['output_selection']</filter>
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209 </data>
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210 <data name="annotation_plot" format="svg" from_work_dir="bakta_output/bakta_output.svg" label="${tool.name} on ${on_string}: Plot of the annotation">
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211 <filter>output_files['output_selection'] and "file_plot" in output_files['output_selection']</filter>
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212 </data>
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213 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file">
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214 <filter>output_files['output_selection'] and "log_txt" in output_files['output_selection']</filter>
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215 </data>
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216 </outputs>
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217 <tests>
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218 <test expect_num_outputs="13"> <!-- TEST_1 database + input -->
5
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219 <section name="input_option" >
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220 <param name="bakta_db_select" value="V5.0_2022-08-19"/>
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221 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
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222 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
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223 <param name="min_contig_length" value="250"/>
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224 </section>
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225 <section name="output_files">
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226 <param name="output_selection" value="file_tsv,file_gff3,file_gbff,file_embl,file_fna,file_ffn,file_faa,hypo_tsv,hypo_fa,sum_txt,file_json,file_plot,log_txt"/>
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227 </section>
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228 <output name="annotation_tsv" value="TEST_1/TEST_1.tsv" lines_diff="2"/>
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229 <output name="annotation_gff3" value="TEST_1/TEST_1.gff3" lines_diff="2"/>
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230 <output name="annotation_gbff" value="TEST_1/TEST_1.gbff" lines_diff="8"/>
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231 <output name="annotation_embl" value="TEST_1/TEST_1.embl" lines_diff="6"/>
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232 <output name="annotation_fna" value="TEST_1/TEST_1.fna"/>
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233 <output name="annotation_ffn" value="TEST_1/TEST_1.ffn"/>
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234 <output name="annotation_faa" value="TEST_1/TEST_1.faa"/>
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235 <output name="hypotheticals_tsv" value="TEST_1/TEST_1.hypotheticals.tsv" lines_diff="4"/>
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236 <output name="hypotheticals_faa" value="TEST_1/TEST_1.hypotheticals.faa"/>
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237 <output name="summary_txt" value="TEST_1/TEST_1.txt" lines_diff="4"/>
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238 <output name="annotation_plot" value="TEST_1/TEST_1_plot.svg" ftype="svg" compare="sim_size"/>
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239 <output name="annotation_json" value="TEST_1/TEST_1.json" lines_diff="6"/>
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240 <output name="logfile" ftype="txt">
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241 <expand macro="assert_content_test"/>
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242 </output>
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243 </test>
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244 <test expect_num_outputs="4"> <!-- TEST_2 another input, add organism info some annotations and skip 2 steps -->
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245 <section name="input_option" >
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246 <param name="bakta_db_select" value="V5.0_2022-08-19"/>
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247 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
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248 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
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249 <param name="min_contig_length" value="250"/>
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250 </section>
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251 <section name="organism">
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252 <param name="genus" value="Escherichia"/>
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253 <param name="species" value="coli O157:H7"/>
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254 <param name="strain" value="Sakai"/>
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255 <param name="plasmid" value="pOSAK1"/>
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256 </section>
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257 <section name="annotation">
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258 <param name="keep_contig_headers" value="true"/>
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259 </section>
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260 <section name="workflow">
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261 <param name="skip_analysis" value="--skip-trna,--skip-tmrna"/>
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262 </section>
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263 <output name="annotation_tsv" value="TEST_2/TEST_2.tsv" lines_diff="4">
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264 <assert_contents>
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265 <has_text_matching expression="IHHALP_00005"/>
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266 </assert_contents>
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267 </output>
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268 <output name="annotation_gff3" value="TEST_2/TEST_2.gff3" lines_diff="4">
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269 <assert_contents>
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270 <has_text_matching expression="ID=NC_002127.1;Name=NC_002127.1;Is_circular=true"/>
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271 </assert_contents>
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272 </output>
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273 <output name="annotation_ffn" value="TEST_2/TEST_2.ffn"/>
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274 <output name="annotation_plot" value="TEST_2/TEST_2_plot.svg" ftype="svg" compare="sim_size"/>
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275 </test>
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276 <test expect_num_outputs="4"> <!-- TEST_3 test all skip steps -->
4
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277 <section name="input_option" >
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278 <param name="bakta_db_select" value="V5.0_2022-08-19"/>
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279 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
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280 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
5
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281 <param name="min_contig_length" value="350"/>
4
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282 </section>
5
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283 <section name="workflow">
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284 <param name="skip_analysis" value="--skip-trna,--skip-tmrna,--skip-rrna,--skip-ncrna,--skip-ncrna-region,--skip-crispr,--skip-cds,--skip-sorf,--skip-gap,--skip-ori,--skip-plot"/>
4
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285 </section>
5
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286 <output name="annotation_tsv" value="TEST_3/TEST_3.tsv" lines_diff="4"/>
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287 <output name="annotation_gff3" value="TEST_3/TEST_3.gff3" lines_diff="4"/>
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288 <output name="annotation_ffn" value="TEST_3/TEST_3.ffn"/>
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289 </test>
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290 <test expect_num_outputs="4"> <!-- TEST_4 annotations -->
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291 <section name="input_option" >
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292 <param name="bakta_db_select" value="V5.0_2022-08-19"/>
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293 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
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294 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
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295 </section>
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296 <section name="annotation">
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297 <param name="complete" value="true"/>
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298 <param name="prodigal" value="prodigal.tf"/>
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299 <param name="translation_table" value="4"/>
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300 <param name="replicons" value="replicons.tsv" ftype="tabular"/>
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301 <param name="compliant" value="true"/>
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302 <param name="proteins" value="user-proteins.faa" ftype="fasta"/>
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303 </section>
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304 <output name="annotation_tsv" value="TEST_4/TEST_4.tsv" lines_diff="4"/>
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305 <output name="annotation_gff3" value="TEST_4/TEST_4.gff3" lines_diff="4"/>
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306 <output name="annotation_ffn" value="TEST_4/TEST_4.ffn"/>
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307 <output name="annotation_plot" value="TEST_4/TEST_4_plot.svg" ftype="svg" compare="sim_size"/>
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308 </test>
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309 <test expect_num_outputs="2"> <!-- TEST_5 skip all steps and keep only the logfile and summary -->
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310 <section name="input_option" >
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311 <param name="bakta_db_select" value="V5.0_2022-08-19"/>
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312 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
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313 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
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314 </section>
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315 <section name="annotation">
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316 <param name="complete" value="true"/>
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317 <param name="translation_table" value="4"/>
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318 </section>
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319 <section name="workflow">
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320 <param name="skip_analysis" value="--skip-trna,--skip-tmrna,--skip-rrna,--skip-ncrna,--skip-ncrna-region,--skip-crispr,--skip-cds,--skip-sorf,--skip-gap,--skip-ori,--skip-plot"/>
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321 </section>
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322 <section name="output_files">
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323 <param name="output_selection" value="log_txt,sum_txt"/>
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324 </section>
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325 <output name="logfile" ftype="txt">
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326 <expand macro="assert_content_test"/>
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327 </output>
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328 <output name="summary_txt" value="TEST_5/TEST_5.txt" lines_diff="4"/>
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329 </test>
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330 <test expect_num_outputs="13"> <!-- TEST_6 metagenome option -->
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331 <section name="input_option" >
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332 <param name="bakta_db_select" value="V5.0_2022-08-19"/>
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333 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
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334 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
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335 </section>
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336 <section name="annotation">
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337 <param name="meta" value="true"/>
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338 </section>
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339 <section name="output_files">
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340 <param name="output_selection" value="file_tsv,file_gff3,file_gbff,file_embl,file_fna,file_ffn,file_faa,hypo_tsv,hypo_fa,sum_txt,file_json,file_plot,log_txt"/>
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
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341 </section>
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342 <output name="annotation_tsv" value="TEST_6/TEST_6.tsv" lines_diff="2"/>
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343 <output name="annotation_gff3" value="TEST_6/TEST_6.gff3" lines_diff="2"/>
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344 <output name="annotation_gbff" value="TEST_6/TEST_6.gbff" lines_diff="8"/>
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345 <output name="annotation_embl" value="TEST_6/TEST_6.embl" lines_diff="6"/>
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346 <output name="annotation_fna" value="TEST_6/TEST_6.fna"/>
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347 <output name="annotation_ffn" value="TEST_6/TEST_6.ffn"/>
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348 <output name="annotation_faa" value="TEST_6/TEST_6.faa"/>
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349 <output name="hypotheticals_tsv" value="TEST_6/TEST_6.hypotheticals.tsv" lines_diff="4"/>
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350 <output name="hypotheticals_faa" value="TEST_6/TEST_6.hypotheticals.faa"/>
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351 <output name="summary_txt" value="TEST_6/TEST_6.txt" lines_diff="4"/>
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352 <output name="annotation_plot" value="TEST_6/TEST_6_plot.svg" ftype="svg" compare="sim_size"/>
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353 <output name="annotation_json" value="TEST_6/TEST_6.json" lines_diff="6"/>
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354 <output name="logfile" ftype="txt">
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355 <expand macro="assert_content_test"/>
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356 </output>
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357 </test>
0
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358 </tests>
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359 <help><![CDATA[**What it does**
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360 Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.
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361
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362 *Comprehensive & taxonomy-independent database*
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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363 Bakta provides a large and taxonomy-independent database using UniProt's entire UniRef protein sequence cluster universe.
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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364
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365 *Protein sequence identification*
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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366 Bakta exactly identifies known identical protein sequences (IPS) from RefSeq and UniProt
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367 allowing the fine-grained annotation of gene alleles (AMR) or closely related but distinct protein families.
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368 This is achieved via an alignment-free sequence identification (AFSI) approach
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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369 using full-length MD5 protein sequence hash digests.
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370 *Small proteins/short open reading frames*
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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371 Bakta detects and annotates small proteins/short open reading frames (sORF).
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372
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373 *Expert annotation systems*
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374 To provide high quality annotations for certain proteins of higher interest, e.g. AMR & VF genes,
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375 Bakta includes & merges different expert annotation systems.
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376 Currently, Bakta uses NCBI's AMRFinderPlus for AMR gene annotations
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377 as well as an generalized protein sequence expert system with distinct
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378 coverage, identity and priority values for each sequence, currenlty comprising the VFDB as well as NCBI's BlastRules.
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379
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380 *Comprehensive workflow*
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381 Bakta annotates ncRNA cis-regulatory regions, oriC/oriV/oriT
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382 and assembly gaps as well as standard feature types: tRNA, tmRNA, rRNA, ncRNA genes, CRISPR, CDS.
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383
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384 *GFF3 & INSDC conform annotations*
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385 Bakta writes GFF3 and INSDC-compliant (Genbank & EMBL) annotation files ready for submission
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386 (checked via GenomeTools GFF3Validator, table2asn_GFF and ENA Webin-CLI for GFF3 and EMBL file formats,
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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387 respectively for representative genomes of all ESKAPE species).
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388
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389 *Bacteria & plasmids*
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390 Bakta was designed to annotate bacteria (isolates & MAGs) and plasmids, only.
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391
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392 **Input options**
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393 1. Choose a genome or assembly in fasta format to use bakta annotations
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394 2. Choose A version of the Bakta database
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395
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396 **Organism options**
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397 You can specify informations about analysed fasta as text input for:
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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398 - genus
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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399 - species
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400 - strain
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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401 - plasmid
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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402
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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403 **Annotation options**
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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404 1. You can specify if all sequences (chromosome or plasmids) are complete or not
2
debdc1469b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
iuc
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405 2. You can add your own prodigal training file for CDS predictionœ
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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406 3. The translation table could be modified, default is the 11th for bacteria
3
865ece5ca178 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
iuc
parents: 2
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407 4. You can specify if bacteria is gram -/+ or unknonw (default value is unknow)
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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408 5. You can keep the name of contig present in the input file
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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409 6. You can specify your own replicon table as a TSV/CSV file
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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410 7. The compliance option is for ready to submit annotation file to Public database
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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411 as ENA, Genbank EMBL
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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412 8. You can specify a protein sequence file for annotation in GenBank or fasta formats
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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413 Using the Fasta format, each reference sequence can be provided in a short or long format:
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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414
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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415 # short:
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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416 >id gene~~~product~~~dbxrefs
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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417 MAQ...
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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418
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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419 # long:
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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420 >id min_identity~~~min_query_cov~~~min_subject_cov~~~gene~~~product~~~dbxrefs
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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421 MAQ...
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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422
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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423 **Skip steps**
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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424 Some steps could be skiped:
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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425 - skip-trna Skip tRNA detection & annotation
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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426 - skip-tmrna Skip tmRNA detection & annotation
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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427 - skip-rrna Skip rRNA detection & annotation
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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428 - skip-ncrna Skip ncRNA detection & annotation
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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429 - skip-ncrna-region Skip ncRNA region detection & annotation
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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430 - skip-crispr Skip CRISPR array detection & annotation
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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431 - skip-cds Skip CDS detection & annotation
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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432 - skip-pseudo Skip pseudogene detection & annotation
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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433 - skip-sorf Skip sORF detection & annotation
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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434 - skip-gap Skip gap detection & annotation
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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435 - skip-ori Skip oriC/oriT detection & annotation
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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436
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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437 **Output options**
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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438 Bakta produce numbers of output files, you can select what type of file you want:
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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439 - Summary of the annotation
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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440 - Annotated files
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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441 - Sequence files for nucleotide and/or amino acid
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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442 ]]></help>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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443 <expand macro="citations"/>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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444 </tool>