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annotate bakta.xml @ 2:debdc1469b41 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
author iuc
date Wed, 21 Dec 2022 20:59:54 +0000
parents da5f1924bb2e
children 865ece5ca178
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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>
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iuc
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3 genome annotation via alignment-free sequence identification
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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8 <expand macro='edam'/>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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"/>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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11 <expand macro="version_command"/>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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[
2
debdc1469b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
iuc
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14 mkdir ./database_path &&
debdc1469b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
iuc
parents: 1
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15 ln -s '$(input_option.bakta_db_select.fields.path)/'* database_path &&
debdc1469b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
iuc
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16 ln -s '$(input_option.amrfinder_db_select.fields.path)' database_path &&
debdc1469b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
iuc
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17
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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18 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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19 #*======================================
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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20 CPU option
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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21 ======================================*#
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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22 --threads \${GALAXY_SLOTS:-1}
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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23 #*======================================
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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24 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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25 ======================================*#
2
debdc1469b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
iuc
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26 --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
iuc
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27 #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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28 --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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29 #else if $annotation.compliant
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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30 --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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31 #else
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 1
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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33 #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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34 --prefix bakta_output
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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35 #*======================================
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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36 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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37 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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38 ======================================*#
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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39 #if $organism.genus
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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40 --genus '$organism.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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41 #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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42 #if $organism.species
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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43 --species '$organism.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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44 #end if
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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45 #if $organism.strain
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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46 --strain '$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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47 #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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48 #if $organism.plasmid
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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49 --plasmid '$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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50 #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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51 #*======================================
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iuc
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52 Annotation options
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iuc
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53 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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54 ======================================*#
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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55 $annotation.complete
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56 #if $annotation.prodigal
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57 --prodigal-tf '$annotation.prodigal'
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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58 #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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59 #if $annotation.translation_table
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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60 --translation-table '$annotation.translation_table'
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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61 #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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62 #if $annotation.gram
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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63 --gram '$annotation.gram'
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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64 #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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65 $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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66 #if $annotation.replicons
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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67 --replicons '$annotation.replicons'
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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68 #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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69 $annotation.compliant
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70 #if $annotation.proteins
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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71 --proteins '$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
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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73 #*======================================
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74 Workflow OPTIONS
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75 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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76 ======================================*#
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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77
2
debdc1469b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
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78 #echo " ".join($workflow.skip_analysis)
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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79
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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80 #*======================================
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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81 Genome file
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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82 ======================================*#
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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83 '$input_option.input_file'
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84 #*======================================
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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85 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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86 ======================================*#
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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87 | 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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88 ]]></command>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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89 <inputs>
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90 <!-- DB and file INPUT -->
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91 <section name="input_option" title="Input/Output options" expanded="true">
2
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92 <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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93 <options from_data_table="bakta_database">
2
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94 <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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95 <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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96 </options>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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97 </param>
2
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98 <param name="amrfinder_db_select" type="select" label="The amrfinderplus database">
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99 <options from_data_table="amrfinderplus_database">
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100 <validator message="No amrfinderplus database is available" type="no_options"/>
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101 </options>
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102 </param>
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103
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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104 <param name="input_file" type="data" format="fasta,fasta.gz" label="Select genome in fasta format"/>
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105 <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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106 </section>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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107 <!-- Organism INFORMATION OPTIONS -->
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108 <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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109 <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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110 <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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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="--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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113 <validator type="regex">^[a-zA-Z0-9\s(:\-/)]+$</validator>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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114 </param>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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115 <param argument="--strain" type="text" optional="true" label="Specify strain name" help="ex. Sakai">
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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116 <validator type="regex">^[a-zA-Z]+$</validator>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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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 <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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119 <validator type="regex">^[a-zA-Z0-9\s(:\-/)]+$</validator>
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120 </param>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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121 </section>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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122 <!-- ANNOTATION -->
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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123 <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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124 <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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125 <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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126 <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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127 <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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128 <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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129 </param>
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130 <param argument="--gram" type="select" optional="true" label="Gram type for signal peptide predictions" help="Gram type +/- or unknown. Default: unknown">
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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131 <option value="+">Gram+</option>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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132 <option value="-">Gram-</option>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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133 <option value="?" selected="true">Unknown</option>
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>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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135 <param name="keep_contig_headers" type="boolean" truevalue="--keep-contig-headers" falsevalue="" label="Keep original contig header (--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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136 <param argument="--replicons" type="data" format="tsv,csv" optional="true" label="Replicon information table (tsv/csv)" help=""/>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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137 <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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138 <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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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">
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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142 <param name="skip_analysis" type="select" display="checkboxes" multiple="true" label="Select steps to skip">
2
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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>
0
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154 </param>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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155 </section>
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156 <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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157 <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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158 <option value="file_tsv" selected="true"> Annotation file in TSV </option>
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159 <option value="file_gff3" selected="true"> Annotation and sequence in GFF3 </option>
2
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160 <option value="file_gbff" selected="false"> Annotations and sequences in GenBank format </option>
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161 <option value="file_embl" selected="false"> Annotations and sequences in EMBL format </option>
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162 <option value="file_fna" selected="false"> Replicon/contig DNA sequences as FASTA </option>
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163 <option value="file_ffn" selected="true"> Feature nucleotide sequences as FASTA </option>
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164 <option value="file_faa" selected="false"> CDS/sORF amino acid sequences as FASTA </option>
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165 <option value="hypo_tsv" selected="false"> Hypothetical protein CDS in TSV</option>
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166 <option value="hypo_fa" selected="false"> Hypothetical protein CDS amino sequences as FASTA</option>
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167 <option value="sum_txt" selected="false"> Summary as TXT</option>
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168 <option value="file_json" selected="false"> Information on each annotated feature as JSON </option>
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169 <option value="file_plot" selected="true"> Plot of the annotation result as SVG </option>
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170 <option value="log_txt" selected="false"> Log file as TXT </option>
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171 </param>
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172 </section>
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173
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174 </inputs>
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175 <outputs>
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176 <data name="annotation_tsv" format="tabular" from_work_dir="bakta_output.tsv" label="${tool.name} on ${on_string}: annotation_summary">
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177 <filter> output_files['output_selection'] and "file_tsv" in output_files['output_selection'] </filter>
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178 </data>
2
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179 <data name="annotation_gff3" format="gff3" from_work_dir="bakta_output.gff3" label="${tool.name} on ${on_string}: Annotation_and_sequences">
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180 <filter> output_files['output_selection'] and "file_gff3" in output_files['output_selection'] </filter>
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181 </data>
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182 <data name="annotation_gbff" format="tabular" from_work_dir="bakta_output.gbff" label="${tool.name} on ${on_string}: bakta_output.gbff">
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183 <filter> output_files['output_selection'] and "file_gbff" in output_files['output_selection'] </filter>
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184 </data>
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185 <data name="annotation_embl" format="tabular" from_work_dir="bakta_output.embl" label="${tool.name} on ${on_string}: bakta_output.embl">
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186 <filter> output_files['output_selection'] and "file_embl" in output_files['output_selection'] </filter>
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187 </data>
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188 <data name="annotation_fna" format="fasta" from_work_dir="bakta_output.fna" label="${tool.name} on ${on_string}: Contig_sequences">
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189 <filter> output_files['output_selection'] and "file_fna" in output_files['output_selection'] </filter>
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190 </data>
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191 <data name="annotation_ffn" format="fasta" from_work_dir="bakta_output.ffn" label="${tool.name} on ${on_string}: Nucleotide_sequences">
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192 <filter> output_files['output_selection'] and "file_ffn" in output_files['output_selection'] </filter>
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193 </data>
2
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194 <data name="annotation_faa" format="fasta" from_work_dir="bakta_output.faa" label="${tool.name} on ${on_string}: Amino_acid_sequences">
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195 <filter> output_files['output_selection'] and "file_faa" in output_files['output_selection'] </filter>
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196 </data>
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197 <data name="hypotheticals_tsv" format="tabular" from_work_dir="bakta_output.hypotheticals.tsv" label="${tool.name} on ${on_string}: hypothetical_annotation_summary">
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198 <filter> output_files['output_selection'] and "hypo_tsv" in output_files['output_selection'] </filter>
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199 </data>
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200 <data name="hypotheticals_faa" format="fasta" from_work_dir="bakta_output.hypotheticals.faa" label="${tool.name} on ${on_string}: hypothetical_amino_acid_sequences">
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201 <filter> output_files['output_selection'] and "hypo_fa" in output_files['output_selection'] </filter>
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202 </data>
2
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203 <data name="summary_txt" format="txt" from_work_dir="bakta_output.txt" label="${tool.name} on ${on_string}: Analysis_summary">
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204 <filter> output_files['output_selection'] and "sum_txt" in output_files['output_selection'] </filter>
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205 </data>
2
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206 <data name="annotation_json" format="json" from_work_dir="bakta_output.json" label="${tool.name} on ${on_string}: annotation_machine_readable">
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207 <filter> output_files['output_selection'] and "file_json" in output_files['output_selection'] </filter>
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208 </data>
2
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209 <data name="annotation_plot" format="svg" from_work_dir="bakta_output.svg" label="${tool.name} on ${on_string}: Plot of the annotation">
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210 <filter> output_files['output_selection'] and "file_plot" in output_files['output_selection'] </filter>
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211 </data>
0
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212 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file">
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213 <filter> output_files['output_selection'] and "log_txt" in output_files['output_selection'] </filter>
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214 </data>
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215 </outputs>
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216 <tests>
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217 <test expect_num_outputs="13"> <!-- TEST_1 database + input -->
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218 <section name="input_option" >
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219 <param name="bakta_db_select" value="V0.1_2022-08-29"/>
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220 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
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221 <param name="input_file" value="NC_002127.1.fna"/>
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222 <param name="min_contig_length" value="250"/>
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223 </section>
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224 <section name="output_files">
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225 <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"/>
debdc1469b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
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226 </section>
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227 <output name="annotation_tsv" value="TEST_1/TEST_1.tsv" lines_diff="2"/>
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228 <output name="annotation_gff3" value="TEST_1/TEST_1.gff3" lines_diff="2"/>
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229 <output name="annotation_gbff" value="TEST_1/TEST_1.gbff" lines_diff="8"/>
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230 <output name="annotation_embl" value="TEST_1/TEST_1.embl" lines_diff="6"/>
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231 <output name="annotation_fna" value="TEST_1/TEST_1.fna"/>
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232 <output name="annotation_ffn" value="TEST_1/TEST_1.ffn"/>
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233 <output name="annotation_faa" value="TEST_1/TEST_1.faa"/>
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234 <output name="hypotheticals_tsv" value="TEST_1/TEST_1.hypotheticals.tsv" lines_diff="4"/>
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235 <output name="hypotheticals_faa" value="TEST_1/TEST_1.hypotheticals.faa"/>
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236 <output name="summary_txt" value="TEST_1/TEST_1.txt" lines_diff="4"/>
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237 <output name="annotation_plot">
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238 <assert_contents>
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239 <has_size value="418991" delta="1000"/>
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240 </assert_contents>
0
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241 </output>
2
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242
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243 <output name="annotation_json" value="TEST_1/TEST_1.json" lines_diff="6"/>
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244 <output name="logfile" value="TEST_1/TEST_1.log" lines_diff="6"/>
0
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245 </test>
2
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246 <test expect_num_outputs="4"> <!-- TEST_2 another input, add organism info some annotations and skip 2 steps -->
0
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247 <section name="input_option" >
2
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248 <param name="bakta_db_select" value="V0.1_2022-08-29"/>
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249 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
0
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250 <param name="input_file" value="NC_002127.1.fna"/>
2
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251 <param name="min_contig_length" value="250"/>
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252 </section>
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253 <section name="organism">
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254 <param name="genus" value="Escherichia"/>
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255 <param name="species" value="coli O157:H7"/>
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256 <param name="strain" value="Sakai"/>
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257 <param name="plasmid" value="pOSAK1"/>
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258 </section>
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259 <section name="annotation">
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260 <param name="--gram" value="-"/>
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261 <param name="keep_contig_headers" value="true"/>
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262 </section>
2
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263 <section name="workflow">
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264 <param name="skip_analysis" value="--skip-trna,--skip-tmrna"/>
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265 </section>
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266 <output name="annotation_tsv" value="TEST_2/TEST_2.tsv" lines_diff="4">
0
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267 <assert_contents>
2
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268 <has_text_matching expression="IHHALP_00005"/>
0
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269 </assert_contents>
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270 </output>
2
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271 <output name="annotation_gff3" value="TEST_2/TEST_2.gff3" lines_diff="4">
0
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272 <assert_contents>
2
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273 <has_text_matching expression="ID=NC_002127.1;Name=NC_002127.1;Is_circular=true"/>
0
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274 </assert_contents>
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275 </output>
2
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276 <output name="annotation_ffn" value="TEST_2/TEST_2.ffn"/>
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277 <output name="annotation_plot">
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278 <assert_contents>
2
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279 <has_size value="418991" delta="1000"/>
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280 </assert_contents>
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281 </output>
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282 </test>
2
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283 <test expect_num_outputs="4"> <!-- TEST_3 test all skip steps -->
0
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284 <section name="input_option" >
2
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285 <param name="bakta_db_select" value="V0.1_2022-08-29"/>
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286 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
0
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287 <param name="input_file" value="NC_002127.1.fna"/>
2
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288 <param name="min_contig_length" value="350"/>
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289 </section>
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290 <section name="workflow">
2
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291 <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"/>
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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292 </section>
2
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293 <output name="annotation_tsv" value="TEST_3/TEST_3.tsv" lines_diff="4"/>
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294 <output name="annotation_gff3" value="TEST_3/TEST_3.gff3" lines_diff="4"/>
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295 <output name="annotation_ffn" value="TEST_3/TEST_3.ffn"/>
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296 <output name="annotation_plot">
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297 <assert_contents>
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298 <has_size value="418399" delta="1000"/>
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299 </assert_contents>
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300 </output>
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301 </test>
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302 <test expect_num_outputs="4"> <!-- TEST_4 annotations -->
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303 <section name="input_option" >
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304 <param name="bakta_db_select" value="V0.1_2022-08-29"/>
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305 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
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306 <param name="input_file" value="NC_002127.1.fna"/>
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307 </section>
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308 <section name="annotation">
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309 <param name="complete" value="true"/>
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310 <param name="prodigal" value="prodigal.tf"/>
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311 <param name="translation_table" value="4"/>
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312 <param name="replicons" value="replicons.tsv"/>
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313 <param name="compliant" value="true"/>
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314 <param name="proteins" value="user-proteins.faa"/>
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315 </section>
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316 <output name="annotation_tsv" value="TEST_4/TEST_4.tsv" lines_diff="4"/>
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317 <output name="annotation_gff3" value="TEST_4/TEST_4.gff3" lines_diff="4"/>
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318 <output name="annotation_ffn" value="TEST_4/TEST_4.ffn"/>
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319 <output name="annotation_plot">
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320 <assert_contents>
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321 <has_size value="418399" delta="1000"/>
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322 </assert_contents>
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323 </output>
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324 </test>
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325 <test expect_num_outputs="2"> <!-- TEST_5 skip all steps and keep only the logfile and summary -->
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326 <section name="input_option" >
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327 <param name="bakta_db_select" value="V0.1_2022-08-29"/>
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328 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/>
debdc1469b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
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329 <param name="input_file" value="NC_002127.1.fna"/>
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330 </section>
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331 <section name="annotation">
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332 <param name="complete" value="true"/>
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333 <param name="translation_table" value="4"/>
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334 </section>
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335 <section name="workflow">
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336 <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"/>
debdc1469b41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
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337 </section>
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338 <section name="output_files">
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339 <param name="output_selection" value="log_txt,sum_txt"/>
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340 </section>
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341 <output name="logfile" value="TEST_5/TEST_5.log" lines_diff="6"/>
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342 <output name="summary_txt" value="TEST_5/TEST_5.txt" lines_diff="4"/>
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343 </test>
0
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344 </tests>
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345 <help><![CDATA[**What it does**
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346 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
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347
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348 *Comprehensive & taxonomy-independent database*
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349 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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350
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351 *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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352 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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353 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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354 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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355 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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356 *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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357 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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358
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359 *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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360 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
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361 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
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362 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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363 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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364 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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365
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366 *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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367 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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368 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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369
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370 *GFF3 & INSDC conform annotations*
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 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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372 (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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373 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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374
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375 *Bacteria & plasmids*
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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376 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
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377
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378 **Input options**
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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379 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
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380 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
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381
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382 **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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383 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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384 - genus
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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385 - species
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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386 - strain
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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387 - plasmid
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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388
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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389 **Annotation options**
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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390 1. You can specify if all sequences (chromosome or plasmids) are complete or not
2
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391 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
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392 3. The translation table could be modified, default is the 11th for bacteria
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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393 4. You can specify if bacteria is gram -/+ or unknonw (default value unknow)
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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394 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
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395 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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396 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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397 as ENA, Genbank EMBL
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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398 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
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399 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
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400
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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401 # short:
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
402 >id gene~~~product~~~dbxrefs
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
403 MAQ...
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
404
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
405 # long:
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
406 >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
parents:
diff changeset
407 MAQ...
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
408
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
409 **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
410 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
411 - 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
412 - 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
413 - 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
414 - 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
parents:
diff changeset
415 - 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
parents:
diff changeset
416 - 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
parents:
diff changeset
417 - 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
parents:
diff changeset
418 - 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
parents:
diff changeset
419 - 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
parents:
diff changeset
420 - 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
parents:
diff changeset
421 - 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
parents:
diff changeset
422
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
423 **Output options**
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
424 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
parents:
diff changeset
425 - Summary of the annotation
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
426 - Annotated files
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
427 - 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
parents:
diff changeset
428 ]]></help>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
429 <expand macro="citations"/>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
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430 </tool>