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annotate bakta.xml @ 7:ba6990f72184 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
author iuc
date Wed, 05 Jun 2024 14:22:02 +0000
parents 92eee5f31117
children
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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>
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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3 Rapid and standardized annotation of bacterial genomes, MAGs and plasmids
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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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4 </description>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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5 <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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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>
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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8 <expand macro="xrefs"/>
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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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9 <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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10 <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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11 <command detect_errors="aggressive"><![CDATA[
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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12 mkdir -p ./database_path/amrfinderplus-db &&
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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13 ln -s '$(input_option.bakta_db_select.fields.path)'/* database_path &&
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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14 ln -s '$(input_option.amrfinder_db_select.fields.path)/' database_path/amrfinderplus-db/latest &&
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3f0aa1b3e816 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
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15
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ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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16 bakta
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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17 --verbose
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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18 #*======================================
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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19 CPU option
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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20 ======================================*#
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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21 --threads \${GALAXY_SLOTS:-1}
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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22 #*======================================
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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23 Bakta database
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
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24 ======================================*#
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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25 --db './database_path'
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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26 --output 'bakta_output'
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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27 #if $input_option.min_contig_length
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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28 --min-contig-length $input_option.min_contig_length
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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29 #else if $annotation.compliant
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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30 --min-contig-length 200
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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31 #else
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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32 --min-contig-length 1
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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33 #end if
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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34 --prefix bakta_output
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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35 #*======================================
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
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36 Organism options
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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37 genus/species/strain/plasmid
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
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38 ======================================*#
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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39 #if $organism.genus
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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40 --genus '$organism.genus'
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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41 #end if
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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42 #if $organism.species
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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43 --species '$organism.species'
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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44 #end if
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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45 #if $organism.strain
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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46 --strain '$organism.strain'
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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47 #end if
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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48 #if $organism.plasmid
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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49 --plasmid '$organism.plasmid'
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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50 #end if
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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51 #*======================================
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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52 Annotation options
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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53 gram type, prodigal/protein file
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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54 ======================================*#
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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55 $annotation.complete
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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56 #if $annotation.prodigal
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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57 --prodigal-tf '$annotation.prodigal'
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
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58 #end if
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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59 #if $annotation.translation_table
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
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60 --translation-table '$annotation.translation_table'
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
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61 #end if
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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62 --gram '?'
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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63 $annotation.keep_contig_headers
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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64 #if $annotation.replicons
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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65 --replicons '$annotation.replicons'
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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66 #end if
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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67 $annotation.compliant
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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68 #if $annotation.proteins
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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69 --proteins '$annotation.proteins'
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
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70 #end if
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
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71 #if $annotation.regions
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
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72 --regions '$annotation.regions'
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
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73 #end if
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
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74 #*======================================
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75 Workflow OPTIONS
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
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76 skip some step of the bakta analysis
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
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77 ======================================*#
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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78
7
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79 #echo " ".join($workflow.skip_analysis)
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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80
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
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81 #*======================================
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82 Genome file
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
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83 ======================================*#
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84 '$input_option.input_file'
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85 #*======================================
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86 LOG file
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
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87 ======================================*#
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88 | tee '$logfile'
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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89 ]]></command>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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90 <inputs>
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91 <!-- DB and file INPUT -->
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92 <section name="input_option" title="Input/Output options" expanded="true">
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93 <param name="input_file" type="data" format="fasta,fasta.gz" label="Select genome in fasta format"/>
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94 <param argument="--min-contig-length" type="integer" optional="true" min="0" label="Minimum contig size" help="Minimum contig size (default = 1; 200 in compliant mode)"/>
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95 <param name="bakta_db_select" type="select" label="Bakta database">
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96 <options from_data_table="bakta_database">
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97 <filter type="static_value" value="@COMPATIBLE_BAKTA_VERSION@" column="bakta_version"/>
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98 <validator message="No bakta database is available" type="no_options"/>
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99 </options>
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100 </param>
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101 <param name="amrfinder_db_select" type="select" optional="true" label="AMRFinderPlus database" help="The selection of this database is not needed if Bakta database version is higher 5.0">
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102 <options from_data_table="amrfinderplus_versioned_database">
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103 <filter type="static_value" value="3.12" column="db_version"/>
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104 <validator message="No AMRFinderPlus database is available" type="no_options"/>
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105 </options>
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106 </param>
0
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107 </section>
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108 <!-- Organism INFORMATION OPTIONS -->
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109 <section name="organism" title="Optional organism options" expanded="false">
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110 <param argument="--genus" type="text" optional="true" label="Specify genus name" help="ex. Escherichia">
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111 <validator type="regex">^[a-zA-Z]+$</validator>
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112 </param>
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113 <param argument="--species" type="text" optional="true" label="Specify species name" help="ex. 'coli O157:H7'">
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114 <validator type="regex">^[a-zA-Z0-9\s(:\-/)]+$</validator>
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115 </param>
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116 <param argument="--strain" type="text" optional="true" label="Specify strain name" help="ex. Sakai">
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117 <validator type="regex">^[a-zA-Z]+$</validator>
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118 </param>
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119 <param argument="--plasmid" type="text" optional="true" label="Specify plasmid name" help="ex. pOSAK1">
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120 <validator type="regex">^[a-zA-Z0-9\s(:\-/)]+$</validator>
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121 </param>
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122 </section>
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123 <!-- ANNOTATION -->
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124 <section name="annotation" title="Optional annotation">
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125 <param argument="--complete" type="boolean" truevalue="--complete" falsevalue="" label="Complete replicons" help="All sequences are complete replicons (chromosome/plasmid[s])"/>
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126 <param argument="--prodigal" type="data" format="txt" optional="true" label="Prodigal file" help="Prodigal training file for CDS prediction"/>
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127 <param name="translation_table" type="select" optional="true" label="Translation table" help="Default is the bacterial table 11">
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128 <option value="4">4 Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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129 <option value="11" selected="true">11 Bacterial, Archaeal and Plant Plastid Code</option>
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130 </param>
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131 <param argument="--keep-contig-headers" type="boolean" truevalue="--keep-contig-headers" falsevalue="" label="Keep original contig header"/>
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132 <param argument="--replicons" type="data" format="tabular,csv" optional="true" label="Replicon information table (tsv/csv)" help=""/>
0
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133 <param argument="--compliant" type="boolean" truevalue="--compliant" falsevalue="" label="Force Genbank/ENA/DDJB compliance"/>
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134 <param argument="--proteins" type="data" format="fasta" optional="true" label="Protein fasta file" help="Fasta file of trusted protein sequences for CDS annotation"/>
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135 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" label="Metagenome mode" help="Run in metagenome mode. This only affects CDS prediction"/>
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136 <param argument="--regions" type="data" format="gff,genbank" optional="true" label="Pre-annotated regions" help="Regions only, no functional annotations."/>
0
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137 </section>
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138 <!-- PARAMETER FOR WORKFLOW ANALYSIS -->
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139 <section name="workflow" title="Workflow option to skip steps">
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140 <param name="skip_analysis" type="select" display="checkboxes" multiple="true" label="Select steps to skip">
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141 <option value="--skip-trna">Skip tRNA detection and annotation</option>
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142 <option value="--skip-tmrna">Skip tmRNA detection and annotation</option>
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143 <option value="--skip-rrna">Skip rRNA detection and annotation</option>
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144 <option value="--skip-ncrna">Skip ncRNA detection and annotation</option>
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145 <option value="--skip-ncrna-region">Skip ncRNA region detection and annotation</option>
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146 <option value="--skip-crispr">Skip CRISPR array detection and annotation</option>
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147 <option value="--skip-cds">Skip CDS detection and annotation</option>
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148 <option value="--skip-pseudo">Skip pseudogene detection and annotation</option>
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149 <option value="--skip-sorf">Skip sORF detection and annotation</option>
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150 <option value="--skip-gap">Skip gap detection and annotation</option>
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151 <option value="--skip-ori">Skip oriC/oriT detection and annotation</option>
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152 <option value="--skip-plot">Skip generation of circular genome plots</option>
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153 </param>
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154 </section>
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155 <section name="output_files" title="Selection of the output files">
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156 <param name="output_selection" type="select" display="checkboxes" multiple="true" label="Output files selection">
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157 <option value="file_tsv" selected="true">Annotation file in TSV</option>
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158 <option value="file_gff3" selected="true">Annotation and sequence in GFF3</option>
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159 <option value="file_gbff" selected="false">Annotations and sequences in GenBank format</option>
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160 <option value="file_embl" selected="false">Annotations and sequences in EMBL format</option>
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161 <option value="file_fna" selected="false">Replicon/contig DNA sequences as FASTA</option>
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162 <option value="file_ffn" selected="true">Feature nucleotide sequences as FASTA</option>
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163 <option value="file_faa" selected="false">CDS/sORF amino acid sequences as FASTA</option>
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164 <option value="hypo_tsv" selected="false">Hypothetical protein CDS in TSV</option>
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165 <option value="hypo_fa" selected="false">Hypothetical protein CDS amino sequences as FASTA</option>
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166 <option value="sum_txt" selected="false">Summary as TXT</option>
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167 <option value="file_json" selected="false">Information on each annotated feature as JSON</option>
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168 <option value="file_plot" selected="true">Plot of the annotation result as SVG</option>
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169 <option value="log_txt" selected="false">Log file as TXT</option>
0
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170 </param>
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171 </section>
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172 </inputs>
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173 <outputs>
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174 <data name="annotation_tsv" format="tabular" from_work_dir="bakta_output/bakta_output.tsv" label="${tool.name} on ${on_string}: Summary">
4
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175 <filter>output_files['output_selection'] and "file_tsv" in output_files['output_selection']</filter>
0
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176 </data>
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177 <data name="annotation_gff3" format="gff3" from_work_dir="bakta_output/bakta_output.gff3" label="${tool.name} on ${on_string}: Annotation and sequences (GFF3)">
4
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178 <filter>output_files['output_selection'] and "file_gff3" in output_files['output_selection']</filter>
0
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179 </data>
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180 <data name="annotation_gbff" format="tabular" from_work_dir="bakta_output/bakta_output.gbff" label="${tool.name} on ${on_string}: Annotations and sequences (GenBank format)">
4
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181 <filter>output_files['output_selection'] and "file_gbff" in output_files['output_selection']</filter>
0
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182 </data>
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183 <data name="annotation_embl" format="tabular" from_work_dir="bakta_output/bakta_output.embl" label="${tool.name} on ${on_string}: Annotations and sequences (EMBL format)">
4
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184 <filter>output_files['output_selection'] and "file_embl" in output_files['output_selection']</filter>
0
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185 </data>
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186 <data name="annotation_fna" format="fasta" from_work_dir="bakta_output/bakta_output.fna" label="${tool.name} on ${on_string}: Replicon/contig DNA sequences">
4
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187 <filter>output_files['output_selection'] and "file_fna" in output_files['output_selection']</filter>
0
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188 </data>
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189 <data name="annotation_ffn" format="fasta" from_work_dir="bakta_output/bakta_output.ffn" label="${tool.name} on ${on_string}: Feature nucleotide sequences">
4
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190 <filter>output_files['output_selection'] and "file_ffn" in output_files['output_selection']</filter>
0
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191 </data>
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192 <data name="annotation_faa" format="fasta" from_work_dir="bakta_output/bakta_output.faa" label="${tool.name} on ${on_string}: CDS/sORF amino acid sequences">
4
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193 <filter>output_files['output_selection'] and "file_faa" in output_files['output_selection']</filter>
0
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194 </data>
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195 <data name="hypotheticals_tsv" format="tabular" from_work_dir="bakta_output/bakta_output.hypotheticals.tsv" label="${tool.name} on ${on_string}: Hypothetical protein CDS summary">
4
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196 <filter>output_files['output_selection'] and "hypo_tsv" in output_files['output_selection']</filter>
0
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197 </data>
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198 <data name="hypotheticals_faa" format="fasta" from_work_dir="bakta_output/bakta_output.hypotheticals.faa" label="${tool.name} on ${on_string}: Hypothetical protein CDS amino sequences">
4
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199 <filter>output_files['output_selection'] and "hypo_fa" in output_files['output_selection']</filter>
0
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200 </data>
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201 <data name="summary_txt" format="txt" from_work_dir="bakta_output/bakta_output.txt" label="${tool.name} on ${on_string}: Summary (TXT)">
4
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202 <filter>output_files['output_selection'] and "sum_txt" in output_files['output_selection']</filter>
0
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203 </data>
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204 <data name="annotation_json" format="json" from_work_dir="bakta_output/bakta_output.json" label="${tool.name} on ${on_string}: Information on each annotated feature (JSON)">
4
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205 <filter>output_files['output_selection'] and "file_json" in output_files['output_selection']</filter>
0
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206 </data>
4
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207 <data name="annotation_plot" format="svg" from_work_dir="bakta_output/bakta_output.svg" label="${tool.name} on ${on_string}: Plot of the annotation">
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208 <filter>output_files['output_selection'] and "file_plot" in output_files['output_selection']</filter>
2
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209 </data>
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210 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: Log file">
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211 <filter>output_files['output_selection'] and "log_txt" in output_files['output_selection']</filter>
0
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212 </data>
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213 </outputs>
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214 <tests>
2
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215 <test expect_num_outputs="13"> <!-- TEST_1 database + input -->
5
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216 <section name="input_option" >
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217 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
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218 <param name="min_contig_length" value="250"/>
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219 <param name="bakta_db_select" value="V5.1_light_2024-01-19"/>
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220 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
5
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221 </section>
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222 <section name="output_files">
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223 <param name="output_selection" value="file_tsv,file_gff3,file_gbff,file_embl,file_fna,file_ffn,file_faa,hypo_tsv,hypo_fa,sum_txt,file_json,file_plot,log_txt"/>
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
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224 </section>
7
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225 <output name="annotation_tsv" ftype="tabular">
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226 <assert_contents>
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227 <has_n_lines n="8"/>
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228 <has_text text="IHHALP_00005"/>
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229 <has_text text="hypothetical protein"/>
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230 </assert_contents>
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diff changeset
231 </output>
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232 <output name="annotation_gff3" ftype="gff3">
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diff changeset
233 <assert_contents>
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234 <has_n_lines n="36"/>
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235 <has_text text="Prodigal"/>
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236 <has_text text="ID=IHHALP_00005;Name=hypothetical protein;locus_tag=IHHALP_00005;product=hypothetical protein"/>
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237 </assert_contents>
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238 </output>
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239 <output name="annotation_gbff" ftype="tabular">
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240 <assert_contents>
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241 <has_n_lines n="81"/>
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242 <has_text text="DEFINITION"/>
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243 <has_text text="/inference"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
244 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
245 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
246 <output name="annotation_embl" ftype="tabular">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
247 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
248 <has_text text="##Genome Annotation Summary:##"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
249 <has_text text="/product="/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
250 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
251 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
252 <output name="annotation_fna" ftype="fasta">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
253 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
254 <has_text text=">contig_1"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
255 <has_text text="TCTTCTGCGAG"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
256 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
257 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
258 <output name="annotation_ffn" ftype="fasta">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
259 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
260 <has_text text=">IHHALP_00005 hypothetical protein"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
261 <has_text text="ATGACAAAACGAAGTG"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
262 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
263 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
264 <output name="annotation_faa" ftype="fasta">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
265 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
266 <has_text text=">IHHALP_00005 hypothetical protein"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
267 <has_text text="MTKRSGSNTR"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
268 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
269 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
270 <output name="hypotheticals_tsv" ftype="tabular">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
271 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
272 <has_n_lines n="5"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
273 <has_text text="IHHALP_00010"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
274 <has_text text="Sequence Id"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
275 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
276 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
277 <output name="hypotheticals_faa" ftype="fasta">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
278 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
279 <has_text text=">IHHALP_00010 hypothetical protein"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
280 <has_text text="MNKQQQTALNM"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
281 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
282 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
283 <output name="summary_txt" ftype="txt">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
284 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
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285 <has_text text="coding density: 62.0"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
286 <has_text text="CDSs: 2"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
287 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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diff changeset
288 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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289 <output name="annotation_plot" ftype="svg">
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iuc
parents: 6
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290 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
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291 <has_size value="418990" delta="1000"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
292 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
293 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
294 <output name="annotation_json" ftype="json">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
295 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
296 <has_text text="coding_ratio"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
297 <has_text text="n50"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
298 <has_text text="hypothetical protein"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
299 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
300 </output>
5
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iuc
parents: 4
diff changeset
301 <output name="logfile" ftype="txt">
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iuc
parents: 4
diff changeset
302 <expand macro="assert_content_test"/>
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
303 </output>
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
304 </test>
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
305 <test expect_num_outputs="4"> <!-- TEST_2 another input, add organism info some annotations and skip 2 steps -->
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
306 <section name="input_option" >
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iuc
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diff changeset
307 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
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308 <param name="min_contig_length" value="250"/>
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
309 <param name="bakta_db_select" value="V5.1_light_2024-01-19"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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diff changeset
310 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
5
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
311 </section>
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
312 <section name="organism">
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iuc
parents: 4
diff changeset
313 <param name="genus" value="Escherichia"/>
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
314 <param name="species" value="coli O157:H7"/>
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
315 <param name="strain" value="Sakai"/>
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
316 <param name="plasmid" value="pOSAK1"/>
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
317 </section>
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
318 <section name="annotation">
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iuc
parents: 4
diff changeset
319 <param name="keep_contig_headers" value="true"/>
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
320 </section>
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
321 <section name="workflow">
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
322 <param name="skip_analysis" value="--skip-trna,--skip-tmrna"/>
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
323 </section>
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
324 <output name="annotation_tsv">
5
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
325 <assert_contents>
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
326 <has_n_lines n="8"/>
5
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
327 <has_text_matching expression="IHHALP_00005"/>
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
328 </assert_contents>
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
329 </output>
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
330 <output name="annotation_gff3">
5
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
331 <assert_contents>
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
332 <has_n_lines n="37"/>
5
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
333 <has_text_matching expression="ID=NC_002127.1;Name=NC_002127.1;Is_circular=true"/>
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
334 </assert_contents>
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
335 </output>
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
336 <output name="annotation_ffn" ftype="fasta">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
337 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
338 <has_text text=">IHHALP_00005 hypothetical protein"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
339 <has_text text="ATGACAAAACGAAGTG"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
340 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
341 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
342 <output name="annotation_plot" ftype="svg">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
343 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
344 <has_size value="418990" delta="1000"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
345 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
346 </output>
5
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
347 </test>
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
348 <test expect_num_outputs="4"> <!-- TEST_3 test all skip steps and test previous bakta version -->
4
3f0aa1b3e816 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents: 3
diff changeset
349 <section name="input_option" >
3f0aa1b3e816 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents: 3
diff changeset
350 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
5
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
351 <param name="min_contig_length" value="350"/>
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
352 <param name="bakta_db_select" value="V5.0_2022-08-19"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
353 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
354 </section>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
355 <section name="workflow">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
356 <param name="skip_analysis" value="--skip-trna,--skip-tmrna,--skip-rrna,--skip-ncrna,--skip-ncrna-region,--skip-crispr,--skip-cds,--skip-sorf,--skip-gap,--skip-ori,--skip-plot"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
357 </section>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
358 <output name="annotation_tsv">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
359 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
360 <has_n_lines n="6"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
361 <has_text_matching expression="DbXrefs"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
362 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
363 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
364 <output name="annotation_gff3" ftype="gff3">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
365 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
366 <has_n_lines n="34"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
367 <has_text text=">contig_1"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
368 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
369 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
370 <output name="annotation_ffn" ftype="fasta">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
371 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
372 <has_size value="0"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
373 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
374 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
375 </test>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
376 <test expect_num_outputs="4"> <!-- TEST_4 annotations -->
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
377 <section name="input_option" >
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
378 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
379 <param name="bakta_db_select" value="V5.1_light_2024-01-19"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
380 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
381 </section>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
382 <section name="annotation">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
383 <param name="complete" value="true"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
384 <param name="prodigal" value="prodigal.tf"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
385 <param name="translation_table" value="4"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
386 <param name="replicons" value="replicons.tsv" ftype="tabular"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
387 <param name="compliant" value="true"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
388 <param name="proteins" value="user-proteins.faa" ftype="fasta"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
389 </section>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
390 <output name="annotation_tsv">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
391 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
392 <has_n_lines n="8"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
393 <has_text_matching expression="IHHALP_00005"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
394 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
395 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
396 <output name="annotation_gff3" ftype="gff3">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
397 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
398 <has_n_lines n="13"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
399 <has_text text="Prodigal"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
400 <has_text text="ID=IHHALP_00010_gene;locus_tag=IHHALP_00010"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
401 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
402 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
403 <output name="annotation_ffn" ftype="fasta">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
404 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
405 <has_text text=">IHHALP_00005 hypothetical protein"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
406 <has_text text="ATGACAAAACGAAGTG"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
407 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
408 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
409 <output name="annotation_plot" ftype="svg">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
410 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
411 <has_size value="418990" delta="1000"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
412 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
413 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
414 </test>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
415 <test expect_num_outputs="2"> <!-- TEST_5 skip all steps and keep only the logfile and summary -->
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
416 <section name="input_option" >
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
417 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
418 <param name="bakta_db_select" value="V5.1_light_2024-01-19"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
419 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
420 </section>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
421 <section name="annotation">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
422 <param name="complete" value="true"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
423 <param name="translation_table" value="4"/>
4
3f0aa1b3e816 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents: 3
diff changeset
424 </section>
5
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
425 <section name="workflow">
728dacaf08a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 5ab93133efa5de410e992919c4e841807fb43b55
iuc
parents: 4
diff changeset
426 <param name="skip_analysis" value="--skip-trna,--skip-tmrna,--skip-rrna,--skip-ncrna,--skip-ncrna-region,--skip-crispr,--skip-cds,--skip-sorf,--skip-gap,--skip-ori,--skip-plot"/>
4
3f0aa1b3e816 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents: 3
diff changeset
427 </section>
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
428 <section name="output_files">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
429 <param name="output_selection" value="log_txt,sum_txt"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
430 </section>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
431 <output name="logfile" ftype="txt">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
432 <expand macro="assert_content_test"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
433 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
434 <output name="summary_txt" ftype="txt">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
435 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
436 <has_n_lines n="30"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
437 <has_text text="N50: 1330"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
438 <has_text text="oriTs: 0"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
439 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
440 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
441 </test>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
442 <test expect_num_outputs="13"> <!-- TEST_6 metagenome option -->
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
443 <section name="input_option" >
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
444 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
445 <param name="bakta_db_select" value="V5.1_light_2024-01-19"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
446 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
447 </section>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
448 <section name="annotation">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
449 <param name="meta" value="true"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
450 </section>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
451 <section name="output_files">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
452 <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"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
453 </section>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
454 <output name="annotation_tsv" ftype="tabular">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
455 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
456 <has_n_lines n="8"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
457 <has_text text="IHHALP_00005"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
458 <has_text text="hypothetical protein"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
459 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
460 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
461 <output name="annotation_gff3" ftype="gff3">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
462 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
463 <has_n_lines n="36"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
464 <has_text text="Prodigal"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
465 <has_text text="ID=IHHALP_00005;Name=hypothetical protein;locus_tag=IHHALP_00005;product=hypothetical protein"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
466 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
467 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
468 <output name="annotation_gbff" ftype="tabular">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
469 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
470 <has_n_lines n="81"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
471 <has_text text="DEFINITION"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
472 <has_text text="/inference"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
473 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
474 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
475 <output name="annotation_embl" ftype="tabular">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
476 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
477 <has_text text="##Genome Annotation Summary:##"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
478 <has_text text="/product="/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
479 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
480 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
481 <output name="annotation_fna" ftype="fasta">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
482 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
483 <has_text text=">contig_1"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
484 <has_text text="TCTTCTGCGAG"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
485 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
486 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
487 <output name="annotation_ffn" ftype="fasta">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
488 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
489 <has_text text=">IHHALP_00005 hypothetical protein"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
490 <has_text text="ATGACAAAACGAAGTG"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
491 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
492 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
493 <output name="annotation_faa" ftype="fasta">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
494 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
495 <has_text text=">IHHALP_00005 hypothetical protein"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
496 <has_text text="MTKRSGSNTR"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
497 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
498 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
499 <output name="hypotheticals_tsv" ftype="tabular">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
500 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
501 <has_n_lines n="5"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
502 <has_text text="IHHALP_00010"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
503 <has_text text="Sequence Id"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
504 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
505 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
506 <output name="hypotheticals_faa" ftype="fasta">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
507 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
508 <has_text text=">IHHALP_00010 hypothetical protein"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
509 <has_text text="MNKQQQTALNM"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
510 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
511 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
512 <output name="summary_txt" ftype="txt">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
513 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
514 <has_n_lines n="30"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
515 <has_text text="coding density: 62.0"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
516 <has_text text="CDSs: 2"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
517 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
518 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
519 <output name="annotation_plot" ftype="svg">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
520 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
521 <has_size value="418990" delta="1000"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
522 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
523 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
524 <output name="annotation_json" ftype="json">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
525 <assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
526 <has_text text="coding_ratio"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
527 <has_text text="n50"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
528 <has_text text="hypothetical protein"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
529 </assert_contents>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
530 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
531 <output name="logfile" ftype="txt">
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
532 <expand macro="assert_content_test"/>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
533 </output>
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
534 </test>
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
535 </tests>
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
536 <help><![CDATA[
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
537 **What it does**
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
538
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
539 Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
540
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
541 *Comprehensive & taxonomy-independent database*
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
542 Bakta provides a large and taxonomy-independent database using UniProt's entire UniRef protein sequence cluster universe.
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
543
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
544 *Protein sequence identification*
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
545 Bakta exactly identifies known identical protein sequences (IPS) from RefSeq and UniProt
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
546 allowing the fine-grained annotation of gene alleles (AMR) or closely related but distinct protein families.
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
547 This is achieved via an alignment-free sequence identification (AFSI) approach
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
548 using full-length MD5 protein sequence hash digests.
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
549 *Small proteins/short open reading frames*
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
550 Bakta detects and annotates small proteins/short open reading frames (sORF).
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
551
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
552 *Expert annotation systems*
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
553 To provide high quality annotations for certain proteins of higher interest, e.g. AMR & VF genes,
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
554 Bakta includes & merges different expert annotation systems.
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
555 Currently, Bakta uses NCBI's AMRFinderPlus for AMR gene annotations
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
556 as well as an generalized protein sequence expert system with distinct
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
557 coverage, identity and priority values for each sequence, currenlty comprising the VFDB as well as NCBI's BlastRules.
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
558
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
559 *Comprehensive workflow*
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
560 Bakta annotates ncRNA cis-regulatory regions, oriC/oriV/oriT
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
561 and assembly gaps as well as standard feature types: tRNA, tmRNA, rRNA, ncRNA genes, CRISPR, CDS.
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
562
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
563 *GFF3 & INSDC conform annotations*
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
564 Bakta writes GFF3 and INSDC-compliant (Genbank & EMBL) annotation files ready for submission
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
565 (checked via GenomeTools GFF3Validator, table2asn_GFF and ENA Webin-CLI for GFF3 and EMBL file formats,
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
566 respectively for representative genomes of all ESKAPE species).
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
567
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
568 *Bacteria & plasmids*
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
569 Bakta was designed to annotate bacteria (isolates & MAGs) and plasmids, only.
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
570
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
571 **Input options**
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
572
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
573 1. Choose a genome or assembly in fasta format to use bakta annotations
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
574 2. Choose A version of the Bakta database
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
575
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
576 **Organism options**
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
577 You can specify informations about analysed fasta as text input for:
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
578 - genus
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
579 - species
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
580 - strain
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
581 - plasmid
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
582
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
583 **Annotation options**
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
584 1. You can specify if all sequences (chromosome or plasmids) are complete or not
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
585 2. You can add your own prodigal training file for CDS predictionœ
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
586 3. The translation table could be modified, default is the 11th for bacteria
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
587 4. You can specify if bacteria is gram -/+ or unknonw (default value is unknow)
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
588 5. You can keep the name of contig present in the input file
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
589 6. You can specify your own replicon table as a TSV/CSV file
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
590 7. The compliance option is for ready to submit annotation file to Public database
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
591 as ENA, Genbank EMBL
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
592 8. You can specify a protein sequence file for annotation in GenBank or fasta formats
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
593 Using the Fasta format, each reference sequence can be provided in a short or long format:
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
594
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
595 # short:
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
596 >id gene~~~product~~~dbxrefs
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
597 MAQ...
0
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff changeset
598
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
599 # long:
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
600 >id min_identity~~~min_query_cov~~~min_subject_cov~~~gene~~~product~~~dbxrefs
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
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601 MAQ...
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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602
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
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603 **Skip steps**
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
604 Some steps could be skiped:
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
605 - skip-trna Skip tRNA detection & annotation
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
606 - skip-tmrna Skip tmRNA detection & annotation
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
607 - skip-rrna Skip rRNA detection & annotation
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
608 - skip-ncrna Skip ncRNA detection & annotation
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
609 - skip-ncrna-region Skip ncRNA region detection & annotation
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
610 - skip-crispr Skip CRISPR array detection & annotation
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
611 - skip-cds Skip CDS detection & annotation
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
612 - skip-pseudo Skip pseudogene detection & annotation
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
613 - skip-sorf Skip sORF detection & annotation
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
614 - skip-gap Skip gap detection & annotation
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
615 - skip-ori Skip oriC/oriT detection & annotation
0
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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616
7
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
617 **Output options**
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
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618 Bakta produce numbers of output files, you can select what type of file you want:
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
619 - Summary of the annotation
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
620 - Annotated files
ba6990f72184 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e277883fca66013904bae930f04e7f3be5fcb1a2
iuc
parents: 6
diff changeset
621 - Sequence files for nucleotide and/or amino acid
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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622 ]]></help>
1a27ad3d0cdf planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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623 <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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624 </tool>