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annotate bakta.xml @ 3:865ece5ca178 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
author iuc
date Fri, 10 Feb 2023 14:20:09 +0000
parents debdc1469b41
children 3f0aa1b3e816
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1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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1 <tool id="bakta" name="Bakta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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2 <description>
3
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iuc
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3 Genome annotation via alignment-free sequence identification
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iuc
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4 </description>
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iuc
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5 <macros>
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iuc
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6 <import>macro.xml</import>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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7 </macros>
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iuc
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8 <expand macro='edam'/>
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iuc
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9 <expand macro='xrefs'/>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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10 <expand macro="requirements"/>
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iuc
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11 <expand macro="version_command"/>
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iuc
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12
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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13 <command detect_errors="aggressive"><![CDATA[
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865ece5ca178 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
iuc
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14 mkdir -p ./database_path/amrfinderplus-db &&
865ece5ca178 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
iuc
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15 ln -s '$(input_option.bakta_db_select.fields.path)'/* database_path &&
865ece5ca178 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
iuc
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16 ln -s '$(input_option.amrfinder_db_select.fields.path)/' database_path/amrfinderplus-db/latest &&
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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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17 bakta
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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18 #*======================================
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19 CPU option
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iuc
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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 --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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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 Bakta database
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iuc
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24 ======================================*#
2
debdc1469b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
iuc
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25 --db ./database_path
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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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26 #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
iuc
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27 --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
iuc
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28 #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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29 --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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30 #else
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31 --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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32 #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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33 --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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34 #*======================================
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35 Organism options
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36 genus/species/strain/plasmid
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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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 #if $organism.genus
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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39 --genus '$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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40 #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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41 #if $organism.species
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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42 --species '$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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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 $organism.strain
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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45 --strain '$organism.strain'
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
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47 #if $organism.plasmid
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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48 --plasmid '$organism.plasmid'
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49 #end if
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50 #*======================================
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51 Annotation options
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52 gram type, prodigal/protein file
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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53 ======================================*#
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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54 $annotation.complete
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55 #if $annotation.prodigal
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56 --prodigal-tf '$annotation.prodigal'
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57 #end if
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58 #if $annotation.translation_table
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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59 --translation-table '$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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60 #end if
3
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61 --gram '?'
0
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62 $annotation.keep_contig_headers
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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63 #if $annotation.replicons
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64 --replicons '$annotation.replicons'
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65 #end if
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66 $annotation.compliant
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67 #if $annotation.proteins
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68 --proteins '$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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69 #end if
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70 #*======================================
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71 Workflow OPTIONS
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72 skip some step of the bakta analysis
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73 ======================================*#
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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74
2
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75 #echo " ".join($workflow.skip_analysis)
0
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76
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77 #*======================================
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78 Genome file
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79 ======================================*#
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80 '$input_option.input_file'
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81 #*======================================
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82 LOG file
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83 ======================================*#
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84 | tee '$logfile'
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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85 ]]></command>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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86 <inputs>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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87 <!-- DB and file INPUT -->
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88 <section name="input_option" title="Input/Output options" expanded="true">
2
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89 <param name="bakta_db_select" type="select" label="The bakta database">
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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90 <options from_data_table="bakta_database">
2
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91 <filter type="static_value" value="@BAKTA_VERSION@" column="bakta_version"/>
debdc1469b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
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92 <validator message="No bakta database is available" type="no_options"/>
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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93 </options>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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94 </param>
2
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95 <param name="amrfinder_db_select" type="select" label="The amrfinderplus database">
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96 <options from_data_table="amrfinderplus_database">
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97 <validator message="No amrfinderplus database is available" type="no_options"/>
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98 </options>
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99 </param>
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100
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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101 <param name="input_file" type="data" format="fasta,fasta.gz" label="Select genome in fasta format"/>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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102 <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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103 </section>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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104 <!-- Organism INFORMATION OPTIONS -->
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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105 <section name="organism" title="Optional organism options" expanded="false">
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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106 <param argument="--genus" type="text" optional="true" label="Specify genus name" help="ex. Escherichia">
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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107 <validator type="regex">^[a-zA-Z]+$</validator>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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108 </param>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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109 <param argument="--species" type="text" optional="true" label="Specify species name" help="ex. 'coli O157:H7'">
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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110 <validator type="regex">^[a-zA-Z0-9\s(:\-/)]+$</validator>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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111 </param>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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112 <param argument="--strain" type="text" optional="true" label="Specify strain name" help="ex. Sakai">
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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113 <validator type="regex">^[a-zA-Z]+$</validator>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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114 </param>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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115 <param argument="--plasmid" type="text" optional="true" label="Specify plasmid name" help="ex. pOSAK1">
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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116 <validator type="regex">^[a-zA-Z0-9\s(:\-/)]+$</validator>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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117 </param>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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118 </section>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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119 <!-- ANNOTATION -->
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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120 <section name="annotation" title="Optional annotation">
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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121 <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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122 <param argument="--prodigal" type="data" format="txt" optional="true" label="Prodigal file" help="Prodigal training file for CDS prediction"/>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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123 <param name="translation_table" type="select" optional="true" label="Translation table" help="Default is the bacterial table 11">
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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124 <option value="4">4 Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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125 <option value="11" selected="true">11 Bacterial, Archaeal and Plant Plastid Code</option>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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126 </param>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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127 <param name="keep_contig_headers" type="boolean" truevalue="--keep-contig-headers" falsevalue="" label="Keep original contig header (--keep-contig-headers)"/>
3
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128 <param argument="--replicons" type="data" format="tabular,csv" optional="true" label="Replicon information table (tsv/csv)" help=""/>
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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129 <param argument="--compliant" type="boolean" truevalue="--compliant" falsevalue="" label="Force Genbank/ENA/DDJB compliance"/>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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130 <param argument="--proteins" type="data" format="fasta" optional="true" label="Protein fasta file" help="Fasta file of trusted protein sequences for CDS annotation"/>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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131 </section>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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132 <!-- PARAMETER FOR WORKFLOW ANALYSIS -->
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133 <section name="workflow" title="Workflow option to skip steps">
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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134 <param name="skip_analysis" type="select" display="checkboxes" multiple="true" label="Select steps to skip">
2
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135 <option value="--skip-trna"> Skip tRNA detection and annotation </option>
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136 <option value="--skip-tmrna"> Skip tmRNA detection and annotation </option>
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137 <option value="--skip-rrna"> Skip rRNA detection and annotation </option>
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138 <option value="--skip-ncrna"> Skip ncRNA detection and annotation </option>
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139 <option value="--skip-ncrna-region"> Skip ncRNA region detection and annotation </option>
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140 <option value="--skip-crispr"> Skip CRISPR array detection and annotation </option>
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141 <option value="--skip-cds"> Skip CDS detection and annotation </option>
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142 <option value="--skip-pseudo"> Skip pseudogene detection and annotation </option>
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143 <option value="--skip-sorf"> Skip sORF detection and annotation </option>
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144 <option value="--skip-gap"> Skip gap detection and annotation </option>
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145 <option value="--skip-ori"> Skip oriC/oriT detection and annotation </option>
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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146 </param>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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147 </section>
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148 <section name="output_files" title="Selection of the output files">
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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149 <param name="output_selection" type="select" display="checkboxes" multiple="true" label="Output files selection">
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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150 <option value="file_tsv" selected="true"> Annotation file in TSV </option>
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151 <option value="file_gff3" selected="true"> Annotation and sequence in GFF3 </option>
2
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152 <option value="file_gbff" selected="false"> Annotations and sequences in GenBank format </option>
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153 <option value="file_embl" selected="false"> Annotations and sequences in EMBL format </option>
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154 <option value="file_fna" selected="false"> Replicon/contig DNA sequences as FASTA </option>
0
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155 <option value="file_ffn" selected="true"> Feature nucleotide sequences as FASTA </option>
2
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156 <option value="file_faa" selected="false"> CDS/sORF amino acid sequences as FASTA </option>
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157 <option value="hypo_tsv" selected="false"> Hypothetical protein CDS in TSV</option>
debdc1469b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
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158 <option value="hypo_fa" selected="false"> Hypothetical protein CDS amino sequences as FASTA</option>
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159 <option value="sum_txt" selected="false"> Summary as TXT</option>
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160 <option value="file_json" selected="false"> Information on each annotated feature as JSON </option>
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161 <option value="file_plot" selected="true"> Plot of the annotation result as SVG </option>
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162 <option value="log_txt" selected="false"> Log file as TXT </option>
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163 </param>
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164 </section>
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165
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166 </inputs>
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167 <outputs>
2
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168 <data name="annotation_tsv" format="tabular" from_work_dir="bakta_output.tsv" label="${tool.name} on ${on_string}: annotation_summary">
0
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169 <filter> output_files['output_selection'] and "file_tsv" in output_files['output_selection'] </filter>
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170 </data>
2
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171 <data name="annotation_gff3" format="gff3" from_work_dir="bakta_output.gff3" label="${tool.name} on ${on_string}: Annotation_and_sequences">
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172 <filter> output_files['output_selection'] and "file_gff3" in output_files['output_selection'] </filter>
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173 </data>
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174 <data name="annotation_gbff" format="tabular" from_work_dir="bakta_output.gbff" label="${tool.name} on ${on_string}: bakta_output.gbff">
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175 <filter> output_files['output_selection'] and "file_gbff" in output_files['output_selection'] </filter>
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176 </data>
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177 <data name="annotation_embl" format="tabular" from_work_dir="bakta_output.embl" label="${tool.name} on ${on_string}: bakta_output.embl">
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178 <filter> output_files['output_selection'] and "file_embl" in output_files['output_selection'] </filter>
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179 </data>
2
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180 <data name="annotation_fna" format="fasta" from_work_dir="bakta_output.fna" label="${tool.name} on ${on_string}: Contig_sequences">
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181 <filter> output_files['output_selection'] and "file_fna" in output_files['output_selection'] </filter>
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182 </data>
2
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183 <data name="annotation_ffn" format="fasta" from_work_dir="bakta_output.ffn" label="${tool.name} on ${on_string}: Nucleotide_sequences">
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184 <filter> output_files['output_selection'] and "file_ffn" in output_files['output_selection'] </filter>
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185 </data>
2
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186 <data name="annotation_faa" format="fasta" from_work_dir="bakta_output.faa" label="${tool.name} on ${on_string}: Amino_acid_sequences">
0
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187 <filter> output_files['output_selection'] and "file_faa" in output_files['output_selection'] </filter>
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188 </data>
2
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189 <data name="hypotheticals_tsv" format="tabular" from_work_dir="bakta_output.hypotheticals.tsv" label="${tool.name} on ${on_string}: hypothetical_annotation_summary">
0
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190 <filter> output_files['output_selection'] and "hypo_tsv" in output_files['output_selection'] </filter>
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191 </data>
2
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192 <data name="hypotheticals_faa" format="fasta" from_work_dir="bakta_output.hypotheticals.faa" label="${tool.name} on ${on_string}: hypothetical_amino_acid_sequences">
0
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193 <filter> output_files['output_selection'] and "hypo_fa" in output_files['output_selection'] </filter>
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194 </data>
2
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195 <data name="summary_txt" format="txt" from_work_dir="bakta_output.txt" label="${tool.name} on ${on_string}: Analysis_summary">
0
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196 <filter> output_files['output_selection'] and "sum_txt" in output_files['output_selection'] </filter>
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197 </data>
2
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198 <data name="annotation_json" format="json" from_work_dir="bakta_output.json" label="${tool.name} on ${on_string}: annotation_machine_readable">
0
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199 <filter> output_files['output_selection'] and "file_json" in output_files['output_selection'] </filter>
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200 </data>
2
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201 <data name="annotation_plot" format="svg" from_work_dir="bakta_output.svg" label="${tool.name} on ${on_string}: Plot of the annotation">
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202 <filter> output_files['output_selection'] and "file_plot" in output_files['output_selection'] </filter>
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203 </data>
0
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204 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file">
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205 <filter> output_files['output_selection'] and "log_txt" in output_files['output_selection'] </filter>
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206 </data>
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207 </outputs>
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208 <tests>
2
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209 <test expect_num_outputs="13"> <!-- TEST_1 database + input -->
3
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210 <section name="input_option" >
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211 <param name="bakta_db_select" value="V0.1_2022-08-29"/>
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212 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
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213 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
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214 <param name="min_contig_length" value="250"/>
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215 </section>
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216 <section name="output_files">
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217 <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"/>
865ece5ca178 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
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218 </section>
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219 <output name="annotation_tsv" value="TEST_1/TEST_1.tsv" lines_diff="2"/>
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220 <output name="annotation_gff3" value="TEST_1/TEST_1.gff3" lines_diff="2"/>
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221 <output name="annotation_gbff" value="TEST_1/TEST_1.gbff" lines_diff="8"/>
2
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222 <output name="annotation_embl" value="TEST_1/TEST_1.embl" lines_diff="6"/>
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223 <output name="annotation_fna" value="TEST_1/TEST_1.fna"/>
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224 <output name="annotation_ffn" value="TEST_1/TEST_1.ffn"/>
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225 <output name="annotation_faa" value="TEST_1/TEST_1.faa"/>
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226 <output name="hypotheticals_tsv" value="TEST_1/TEST_1.hypotheticals.tsv" lines_diff="4"/>
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227 <output name="hypotheticals_faa" value="TEST_1/TEST_1.hypotheticals.faa"/>
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228 <output name="summary_txt" value="TEST_1/TEST_1.txt" lines_diff="4"/>
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229 <output name="annotation_plot">
3
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230 <assert_contents>
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231 <has_size value="418991" delta="1000"/>
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232 </assert_contents>
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233 </output>
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234 <output name="annotation_json" value="TEST_1/TEST_1.json" lines_diff="6"/>
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235 <output name="logfile" value="TEST_1/TEST_1.log" lines_diff="6"/>
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236 </test>
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237 <test expect_num_outputs="4"> <!-- TEST_2 another input, add organism info some annotations and skip 2 steps -->
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238 <section name="input_option" >
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239 <param name="bakta_db_select" value="V0.1_2022-08-29"/>
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240 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
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241 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
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242 <param name="min_contig_length" value="250"/>
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243 </section>
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244 <section name="organism">
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245 <param name="genus" value="Escherichia"/>
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246 <param name="species" value="coli O157:H7"/>
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247 <param name="strain" value="Sakai"/>
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248 <param name="plasmid" value="pOSAK1"/>
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249 </section>
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250 <section name="annotation">
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251 <param name="keep_contig_headers" value="true"/>
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252 </section>
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253 <section name="workflow">
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254 <param name="skip_analysis" value="--skip-trna,--skip-tmrna"/>
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255 </section>
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256 <output name="annotation_tsv" value="TEST_2/TEST_2.tsv" lines_diff="4">
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257 <assert_contents>
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258 <has_text_matching expression="IHHALP_00005"/>
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259 </assert_contents>
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260 </output>
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261 <output name="annotation_gff3" value="TEST_2/TEST_2.gff3" lines_diff="4">
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262 <assert_contents>
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263 <has_text_matching expression="ID=NC_002127.1;Name=NC_002127.1;Is_circular=true"/>
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264 </assert_contents>
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265 </output>
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266 <output name="annotation_ffn" value="TEST_2/TEST_2.ffn"/>
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267 <output name="annotation_plot">
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268 <assert_contents>
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269 <has_size value="418991" delta="1000"/>
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270 </assert_contents>
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271 </output>
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272 </test>
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273 <test expect_num_outputs="4"> <!-- TEST_3 test all skip steps -->
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274 <section name="input_option" >
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275 <param name="bakta_db_select" value="V0.1_2022-08-29"/>
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276 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
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277 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
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278 <param name="min_contig_length" value="350"/>
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279 </section>
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280 <section name="workflow">
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281 <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"/>
865ece5ca178 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
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282 </section>
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283 <output name="annotation_tsv" value="TEST_3/TEST_3.tsv" lines_diff="4"/>
865ece5ca178 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
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284 <output name="annotation_gff3" value="TEST_3/TEST_3.gff3" lines_diff="4"/>
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285 <output name="annotation_ffn" value="TEST_3/TEST_3.ffn"/>
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286 <output name="annotation_plot">
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287 <assert_contents>
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288 <has_size value="418399" delta="1000"/>
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289 </assert_contents>
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290 </output>
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291 </test>
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292 <test expect_num_outputs="4"> <!-- TEST_4 annotations -->
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293 <section name="input_option" >
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294 <param name="bakta_db_select" value="V0.1_2022-08-29"/>
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295 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
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296 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
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297 </section>
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298 <section name="annotation">
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299 <param name="complete" value="true"/>
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300 <param name="prodigal" value="prodigal.tf"/>
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301 <param name="translation_table" value="4"/>
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302 <param name="replicons" value="replicons.tsv" ftype="tabular"/>
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303 <param name="compliant" value="true"/>
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304 <param name="proteins" value="user-proteins.faa" ftype="fasta"/>
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305 </section>
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306 <output name="annotation_tsv" value="TEST_4/TEST_4.tsv" lines_diff="4"/>
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307 <output name="annotation_gff3" value="TEST_4/TEST_4.gff3" lines_diff="4"/>
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308 <output name="annotation_ffn" value="TEST_4/TEST_4.ffn"/>
2
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309 <output name="annotation_plot">
3
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310 <assert_contents>
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311 <has_size value="418399" delta="1000"/>
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312 </assert_contents>
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313 </output>
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314 </test>
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315 <test expect_num_outputs="2"> <!-- TEST_5 skip all steps and keep only the logfile and summary -->
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316 <section name="input_option" >
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317 <param name="bakta_db_select" value="V0.1_2022-08-29"/>
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318 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
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319 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
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320 </section>
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321 <section name="annotation">
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322 <param name="complete" value="true"/>
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323 <param name="translation_table" value="4"/>
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parents: 2
diff changeset
324 </section>
865ece5ca178 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
iuc
parents: 2
diff changeset
325 <section name="workflow">
865ece5ca178 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
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326 <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"/>
865ece5ca178 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
iuc
parents: 2
diff changeset
327 </section>
865ece5ca178 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
iuc
parents: 2
diff changeset
328 <section name="output_files">
865ece5ca178 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
iuc
parents: 2
diff changeset
329 <param name="output_selection" value="log_txt,sum_txt"/>
865ece5ca178 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
iuc
parents: 2
diff changeset
330 </section>
865ece5ca178 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
iuc
parents: 2
diff changeset
331 <output name="logfile" value="TEST_5/TEST_5.log" lines_diff="6"/>
865ece5ca178 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
iuc
parents: 2
diff changeset
332 <output name="summary_txt" value="TEST_5/TEST_5.txt" lines_diff="4"/>
865ece5ca178 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
iuc
parents: 2
diff changeset
333 </test>
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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334 </tests>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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335 <help><![CDATA[**What it does**
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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336 Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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337
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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338 *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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339 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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340
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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341 *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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342 Bakta exactly identifies known identical protein sequences (IPS) from RefSeq and UniProt
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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343 allowing the fine-grained annotation of gene alleles (AMR) or closely related but distinct protein families.
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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344 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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345 using full-length MD5 protein sequence hash digests.
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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346 *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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347 Bakta detects and annotates small proteins/short open reading frames (sORF).
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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348
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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349 *Expert annotation systems*
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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350 To provide high quality annotations for certain proteins of higher interest, e.g. AMR & VF genes,
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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351 Bakta includes & merges different expert annotation systems.
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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352 Currently, Bakta uses NCBI's AMRFinderPlus for AMR gene annotations
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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353 as well as an generalized protein sequence expert system with distinct
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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354 coverage, identity and priority values for each sequence, currenlty comprising the VFDB as well as NCBI's BlastRules.
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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355
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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356 *Comprehensive workflow*
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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357 Bakta annotates ncRNA cis-regulatory regions, oriC/oriV/oriT
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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358 and assembly gaps as well as standard feature types: tRNA, tmRNA, rRNA, ncRNA genes, CRISPR, CDS.
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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359
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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360 *GFF3 & INSDC conform annotations*
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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361 Bakta writes GFF3 and INSDC-compliant (Genbank & EMBL) annotation files ready for submission
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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362 (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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363 respectively for representative genomes of all ESKAPE species).
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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diff changeset
364
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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diff changeset
365 *Bacteria & plasmids*
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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366 Bakta was designed to annotate bacteria (isolates & MAGs) and plasmids, only.
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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367
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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368 **Input 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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369 1. Choose a genome or assembly in fasta format to use bakta annotations
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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370 2. Choose A version of the Bakta 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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371
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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diff changeset
372 **Organism 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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373 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
iuc
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diff changeset
374 - genus
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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375 - species
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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376 - strain
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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377 - plasmid
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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378
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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379 **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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380 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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diff changeset
381 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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382 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
diff changeset
383 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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384 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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385 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
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386 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
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387 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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388 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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389 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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diff changeset
390
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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diff changeset
391 # short:
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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diff changeset
392 >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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393 MAQ...
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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parents:
diff changeset
394
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
395 # 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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396 >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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diff changeset
397 MAQ...
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
398
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
399 **Skip steps**
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
400 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
parents:
diff changeset
401 - 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
parents:
diff changeset
402 - 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
parents:
diff changeset
403 - 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
parents:
diff changeset
404 - 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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405 - 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
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406 - 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
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407 - 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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408 - 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
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409 - 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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410 - 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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411 - 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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412
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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413 **Output options**
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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414 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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415 - 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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416 - 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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417 - 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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418 ]]></help>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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419 <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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420 </tool>