Mercurial > repos > thanhlv > bakta
annotate bakta.xml @ 3:c44a580fc872 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
author | thanhlv |
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date | Fri, 28 Apr 2023 18:15:19 +0000 |
parents | 30c7c559d5f6 |
children | 7686d59927cd |
rev | line source |
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0
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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1 <tool id="bakta" name="Bakta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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2 <description> |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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3 Genome annotation via alignment-free sequence identification |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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4 </description> |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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5 <macros> |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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6 <import>macro.xml</import> |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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7 </macros> |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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8 <expand macro="requirements"/> |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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9 <expand macro="version_command"/> |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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10 <command detect_errors="aggressive"><![CDATA[ |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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11 mkdir -p ./database_path/amrfinderplus-db && |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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12 ln -s '$(input_option.bakta_db_select.fields.path)'/* database_path && |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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13 ln -s '$(input_option.amrfinder_db_select.fields.path)/' database_path/amrfinderplus-db/latest && |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
parents:
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14 bakta |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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15 #*====================================== |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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16 CPU option |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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17 ======================================*# |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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18 --threads \${GALAXY_SLOTS:-1} |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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19 #*====================================== |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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20 Bakta database |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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21 ======================================*# |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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22 --db ./database_path |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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23 #if $input_option.min_contig_length |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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24 --min-contig-length $input_option.min_contig_length |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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25 #else if $annotation.compliant |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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26 --min-contig-length 200 |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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27 #else |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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28 --min-contig-length 1 |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
parents:
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29 #end if |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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30 --prefix bakta_output |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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31 #*====================================== |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
parents:
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32 Organism options |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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33 genus/species/strain/plasmid |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
parents:
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34 ======================================*# |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
parents:
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35 #if $organism.genus |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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36 --genus '$organism.genus' |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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37 #end if |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
parents:
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38 #if $organism.species |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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39 --species '$organism.species' |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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40 #end if |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
parents:
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41 #if $organism.strain |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
parents:
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42 --strain '$organism.strain' |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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43 #end if |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
parents:
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44 #if $organism.plasmid |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
parents:
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45 --plasmid '$organism.plasmid' |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
parents:
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46 #end if |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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47 #*====================================== |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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48 Annotation options |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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49 gram type, prodigal/protein file |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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50 ======================================*# |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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parents:
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51 $annotation.complete |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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52 #if $annotation.prodigal |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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53 --prodigal-tf '$annotation.prodigal' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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54 #end if |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
parents:
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55 #if $annotation.translation_table |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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56 --translation-table '$annotation.translation_table' |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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57 #end if |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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58 --gram '?' |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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59 $annotation.keep_contig_headers |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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60 #if $annotation.replicons |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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61 --replicons '$annotation.replicons' |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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62 #end if |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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parents:
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63 $annotation.compliant |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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64 #if $annotation.proteins |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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65 --proteins '$annotation.proteins' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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66 #end if |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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67 #*====================================== |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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68 Workflow OPTIONS |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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69 skip some step of the bakta analysis |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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70 ======================================*# |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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71 |
54ca20519f70
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72 #echo " ".join($workflow.skip_analysis) |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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73 |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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74 #*====================================== |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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75 Genome file |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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76 ======================================*# |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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parents:
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77 '$input_option.input_file' |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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78 #*====================================== |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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79 LOG file |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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80 ======================================*# |
54ca20519f70
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81 | tee '$logfile' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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82 ]]></command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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83 <inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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84 <!-- DB and file INPUT --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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85 <section name="input_option" title="Input/Output options" expanded="true"> |
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86 <param name="bakta_db_select" type="select" label="The bakta database"> |
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87 <options from_data_table="bakta_database"> |
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88 <filter type="static_value" value="@BAKTA_VERSION@" column="bakta_version"/> |
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89 <validator message="No bakta database is available" type="no_options"/> |
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90 </options> |
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91 </param> |
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92 <param name="amrfinder_db_select" type="select" label="The amrfinderplus database"> |
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93 <options from_data_table="amrfinderplus_database"> |
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94 <validator message="No amrfinderplus database is available" type="no_options"/> |
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95 </options> |
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96 </param> |
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97 |
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98 <param name="input_file" type="data" format="fasta,fasta.gz" label="Select genome in fasta format"/> |
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99 <param name="min_contig_length" type="integer" optional="true" min="0" label="Minimum contig size" help="Minimum contig size (default = 1; 200 in compliant mode) (--min-contig-length)"/> |
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100 </section> |
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101 <!-- Organism INFORMATION OPTIONS --> |
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102 <section name="organism" title="Optional organism options" expanded="false"> |
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103 <param argument="--genus" type="text" optional="true" label="Specify genus name" help="ex. Escherichia"> |
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104 <validator type="regex">^[a-zA-Z]+$</validator> |
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105 </param> |
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106 <param argument="--species" type="text" optional="true" label="Specify species name" help="ex. 'coli O157:H7'"> |
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107 <validator type="regex">^[a-zA-Z0-9\s(:\-/)]+$</validator> |
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108 </param> |
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109 <param argument="--strain" type="text" optional="true" label="Specify strain name" help="ex. Sakai"> |
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110 <validator type="regex">^[a-zA-Z]+$</validator> |
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111 </param> |
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112 <param argument="--plasmid" type="text" optional="true" label="Specify plasmid name" help="ex. pOSAK1"> |
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113 <validator type="regex">^[a-zA-Z0-9\s(:\-/)]+$</validator> |
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114 </param> |
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115 </section> |
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116 <!-- ANNOTATION --> |
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117 <section name="annotation" title="Optional annotation"> |
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118 <param argument="--complete" type="boolean" truevalue="--complete" falsevalue="" label="Complete replicons" help="All sequences are complete replicons (chromosome/plasmid[s])"/> |
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119 <param argument="--prodigal" type="data" format="txt" optional="true" label="Prodigal file" help="Prodigal training file for CDS prediction"/> |
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120 <param name="translation_table" type="select" optional="true" label="Translation table" help="Default is the bacterial table 11"> |
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121 <option value="4">4 Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> |
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122 <option value="11" selected="true">11 Bacterial, Archaeal and Plant Plastid Code</option> |
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123 </param> |
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124 <param name="keep_contig_headers" type="boolean" truevalue="--keep-contig-headers" falsevalue="" label="Keep original contig header (--keep-contig-headers)"/> |
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125 <param argument="--replicons" type="data" format="tabular,csv" optional="true" label="Replicon information table (tsv/csv)" help=""/> |
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126 <param argument="--compliant" type="boolean" truevalue="--compliant" falsevalue="" label="Force Genbank/ENA/DDJB compliance"/> |
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127 <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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128 </section> |
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129 <!-- PARAMETER FOR WORKFLOW ANALYSIS --> |
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130 <section name="workflow" title="Workflow option to skip steps"> |
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131 <param name="skip_analysis" type="select" display="checkboxes" multiple="true" label="Select steps to skip"> |
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132 <option value="--skip-trna"> Skip tRNA detection and annotation </option> |
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133 <option value="--skip-tmrna"> Skip tmRNA detection and annotation </option> |
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134 <option value="--skip-rrna"> Skip rRNA detection and annotation </option> |
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135 <option value="--skip-ncrna"> Skip ncRNA detection and annotation </option> |
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136 <option value="--skip-ncrna-region"> Skip ncRNA region detection and annotation </option> |
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137 <option value="--skip-crispr"> Skip CRISPR array detection and annotation </option> |
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138 <option value="--skip-cds"> Skip CDS detection and annotation </option> |
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139 <option value="--skip-pseudo"> Skip pseudogene detection and annotation </option> |
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140 <option value="--skip-sorf"> Skip sORF detection and annotation </option> |
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141 <option value="--skip-gap"> Skip gap detection and annotation </option> |
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142 <option value="--skip-ori"> Skip oriC/oriT detection and annotation </option> |
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143 </param> |
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144 </section> |
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145 <section name="output_files" title="Selection of the output files"> |
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146 <param name="output_selection" type="select" display="checkboxes" multiple="true" label="Output files selection"> |
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147 <option value="file_tsv" selected="true"> Annotation file in TSV </option> |
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148 <option value="file_gff3" selected="true"> Annotation and sequence in GFF3 </option> |
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149 <option value="file_gbff" selected="false"> Annotations and sequences in GenBank format </option> |
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150 <option value="file_embl" selected="false"> Annotations and sequences in EMBL format </option> |
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151 <option value="file_fna" selected="false"> Replicon/contig DNA sequences as FASTA </option> |
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152 <option value="file_ffn" selected="true"> Feature nucleotide sequences as FASTA </option> |
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153 <option value="file_faa" selected="false"> CDS/sORF amino acid sequences as FASTA </option> |
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154 <option value="hypo_tsv" selected="false"> Hypothetical protein CDS in TSV</option> |
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155 <option value="hypo_fa" selected="false"> Hypothetical protein CDS amino sequences as FASTA</option> |
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156 <option value="sum_txt" selected="false"> Summary as TXT</option> |
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157 <option value="file_json" selected="false"> Information on each annotated feature as JSON </option> |
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158 <option value="file_plot" selected="true"> Plot of the annotation result as SVG </option> |
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159 <option value="log_txt" selected="false"> Log file as TXT </option> |
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160 </param> |
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161 </section> |
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162 |
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163 </inputs> |
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164 <outputs> |
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165 <data name="annotation_tsv" format="tabular" from_work_dir="bakta_output.tsv" label="${tool.name} on ${on_string}: annotation_summary"> |
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166 <filter> output_files['output_selection'] and "file_tsv" in output_files['output_selection'] </filter> |
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167 </data> |
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168 <data name="annotation_gff3" format="gff3" from_work_dir="bakta_output.gff3" label="${tool.name} on ${on_string}: Annotation_and_sequences"> |
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169 <filter> output_files['output_selection'] and "file_gff3" in output_files['output_selection'] </filter> |
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170 </data> |
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171 <data name="annotation_gbff" format="tabular" from_work_dir="bakta_output.gbff" label="${tool.name} on ${on_string}: bakta_output.gbff"> |
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172 <filter> output_files['output_selection'] and "file_gbff" in output_files['output_selection'] </filter> |
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173 </data> |
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174 <data name="annotation_embl" format="tabular" from_work_dir="bakta_output.embl" label="${tool.name} on ${on_string}: bakta_output.embl"> |
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175 <filter> output_files['output_selection'] and "file_embl" in output_files['output_selection'] </filter> |
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176 </data> |
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177 <data name="annotation_fna" format="fasta" from_work_dir="bakta_output.fna" label="${tool.name} on ${on_string}: Contig_sequences"> |
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178 <filter> output_files['output_selection'] and "file_fna" in output_files['output_selection'] </filter> |
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179 </data> |
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180 <data name="annotation_ffn" format="fasta" from_work_dir="bakta_output.ffn" label="${tool.name} on ${on_string}: Nucleotide_sequences"> |
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181 <filter> output_files['output_selection'] and "file_ffn" in output_files['output_selection'] </filter> |
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182 </data> |
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183 <data name="annotation_faa" format="fasta" from_work_dir="bakta_output.faa" label="${tool.name} on ${on_string}: Amino_acid_sequences"> |
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184 <filter> output_files['output_selection'] and "file_faa" in output_files['output_selection'] </filter> |
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185 </data> |
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186 <data name="hypotheticals_tsv" format="tabular" from_work_dir="bakta_output.hypotheticals.tsv" label="${tool.name} on ${on_string}: hypothetical_annotation_summary"> |
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187 <filter> output_files['output_selection'] and "hypo_tsv" in output_files['output_selection'] </filter> |
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188 </data> |
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189 <data name="hypotheticals_faa" format="fasta" from_work_dir="bakta_output.hypotheticals.faa" label="${tool.name} on ${on_string}: hypothetical_amino_acid_sequences"> |
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190 <filter> output_files['output_selection'] and "hypo_fa" in output_files['output_selection'] </filter> |
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191 </data> |
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192 <data name="summary_txt" format="txt" from_work_dir="bakta_output.txt" label="${tool.name} on ${on_string}: Analysis_summary"> |
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193 <filter> output_files['output_selection'] and "sum_txt" in output_files['output_selection'] </filter> |
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194 </data> |
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195 <data name="annotation_json" format="json" from_work_dir="bakta_output.json" label="${tool.name} on ${on_string}: annotation_machine_readable"> |
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196 <filter> output_files['output_selection'] and "file_json" in output_files['output_selection'] </filter> |
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197 </data> |
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198 <data name="annotation_plot" format="svg" from_work_dir="bakta_output.svg" label="${tool.name} on ${on_string}: Plot of the annotation"> |
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199 <filter> output_files['output_selection'] and "file_plot" in output_files['output_selection'] </filter> |
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200 </data> |
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201 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file"> |
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202 <filter> output_files['output_selection'] and "log_txt" in output_files['output_selection'] </filter> |
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203 </data> |
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204 </outputs> |
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205 <tests> |
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206 <test expect_num_outputs="13"> <!-- TEST_1 database + input --> |
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207 <section name="input_option" > |
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208 <param name="bakta_db_select" value="V0.1_2022-08-29"/> |
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209 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> |
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210 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/> |
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211 <param name="min_contig_length" value="250"/> |
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212 </section> |
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213 <section name="output_files"> |
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214 <param name="output_selection" value="file_tsv,file_gff3,file_gbff,file_embl,file_fna,file_ffn,file_faa,hypo_tsv,hypo_fa,sum_txt,file_json,file_plot,log_txt"/> |
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215 </section> |
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216 <output name="annotation_tsv" value="TEST_1/TEST_1.tsv" lines_diff="2"/> |
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217 <output name="annotation_gff3" value="TEST_1/TEST_1.gff3" lines_diff="2"/> |
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218 <output name="annotation_gbff" value="TEST_1/TEST_1.gbff" lines_diff="8"/> |
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219 <output name="annotation_embl" value="TEST_1/TEST_1.embl" lines_diff="6"/> |
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220 <output name="annotation_fna" value="TEST_1/TEST_1.fna"/> |
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221 <output name="annotation_ffn" value="TEST_1/TEST_1.ffn"/> |
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222 <output name="annotation_faa" value="TEST_1/TEST_1.faa"/> |
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223 <output name="hypotheticals_tsv" value="TEST_1/TEST_1.hypotheticals.tsv" lines_diff="4"/> |
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224 <output name="hypotheticals_faa" value="TEST_1/TEST_1.hypotheticals.faa"/> |
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225 <output name="summary_txt" value="TEST_1/TEST_1.txt" lines_diff="4"/> |
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226 <output name="annotation_plot"> |
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227 <assert_contents> |
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228 <has_size value="418991" delta="1000"/> |
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229 </assert_contents> |
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230 </output> |
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231 <output name="annotation_json" value="TEST_1/TEST_1.json" lines_diff="6"/> |
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232 <output name="logfile" value="TEST_1/TEST_1.log" lines_diff="6"/> |
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233 </test> |
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234 <test expect_num_outputs="4"> <!-- TEST_2 another input, add organism info some annotations and skip 2 steps --> |
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235 <section name="input_option" > |
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236 <param name="bakta_db_select" value="V0.1_2022-08-29"/> |
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237 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> |
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238 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/> |
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239 <param name="min_contig_length" value="250"/> |
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240 </section> |
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241 <section name="organism"> |
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242 <param name="genus" value="Escherichia"/> |
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243 <param name="species" value="coli O157:H7"/> |
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244 <param name="strain" value="Sakai"/> |
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245 <param name="plasmid" value="pOSAK1"/> |
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246 </section> |
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247 <section name="annotation"> |
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248 <param name="keep_contig_headers" value="true"/> |
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249 </section> |
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250 <section name="workflow"> |
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251 <param name="skip_analysis" value="--skip-trna,--skip-tmrna"/> |
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252 </section> |
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253 <output name="annotation_tsv" value="TEST_2/TEST_2.tsv" lines_diff="4"> |
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254 <assert_contents> |
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255 <has_text_matching expression="IHHALP_00005"/> |
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256 </assert_contents> |
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257 </output> |
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258 <output name="annotation_gff3" value="TEST_2/TEST_2.gff3" lines_diff="4"> |
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259 <assert_contents> |
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260 <has_text_matching expression="ID=NC_002127.1;Name=NC_002127.1;Is_circular=true"/> |
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261 </assert_contents> |
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262 </output> |
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263 <output name="annotation_ffn" value="TEST_2/TEST_2.ffn"/> |
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264 <output name="annotation_plot"> |
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265 <assert_contents> |
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266 <has_size value="418991" delta="1000"/> |
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267 </assert_contents> |
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268 </output> |
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269 </test> |
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270 <test expect_num_outputs="4"> <!-- TEST_3 test all skip steps --> |
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271 <section name="input_option" > |
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272 <param name="bakta_db_select" value="V0.1_2022-08-29"/> |
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273 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> |
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274 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/> |
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275 <param name="min_contig_length" value="350"/> |
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276 </section> |
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277 <section name="workflow"> |
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278 <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"/> |
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279 </section> |
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280 <output name="annotation_tsv" value="TEST_3/TEST_3.tsv" lines_diff="4"/> |
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281 <output name="annotation_gff3" value="TEST_3/TEST_3.gff3" lines_diff="4"/> |
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282 <output name="annotation_ffn" value="TEST_3/TEST_3.ffn"/> |
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283 <output name="annotation_plot"> |
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284 <assert_contents> |
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285 <has_size value="418399" delta="1000"/> |
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286 </assert_contents> |
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287 </output> |
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288 </test> |
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289 <test expect_num_outputs="4"> <!-- TEST_4 annotations --> |
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290 <section name="input_option" > |
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291 <param name="bakta_db_select" value="V0.1_2022-08-29"/> |
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292 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> |
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293 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/> |
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294 </section> |
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295 <section name="annotation"> |
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296 <param name="complete" value="true"/> |
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297 <param name="prodigal" value="prodigal.tf"/> |
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298 <param name="translation_table" value="4"/> |
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299 <param name="replicons" value="replicons.tsv" ftype="tabular"/> |
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300 <param name="compliant" value="true"/> |
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301 <param name="proteins" value="user-proteins.faa" ftype="fasta"/> |
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302 </section> |
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303 <output name="annotation_tsv" value="TEST_4/TEST_4.tsv" lines_diff="4"/> |
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304 <output name="annotation_gff3" value="TEST_4/TEST_4.gff3" lines_diff="4"/> |
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305 <output name="annotation_ffn" value="TEST_4/TEST_4.ffn"/> |
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306 <output name="annotation_plot"> |
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307 <assert_contents> |
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308 <has_size value="418399" delta="1000"/> |
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309 </assert_contents> |
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310 </output> |
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311 </test> |
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312 <test expect_num_outputs="2"> <!-- TEST_5 skip all steps and keep only the logfile and summary --> |
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313 <section name="input_option" > |
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314 <param name="bakta_db_select" value="V0.1_2022-08-29"/> |
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315 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> |
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316 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/> |
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317 </section> |
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318 <section name="annotation"> |
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319 <param name="complete" value="true"/> |
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320 <param name="translation_table" value="4"/> |
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321 </section> |
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322 <section name="workflow"> |
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323 <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"/> |
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324 </section> |
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325 <section name="output_files"> |
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326 <param name="output_selection" value="log_txt,sum_txt"/> |
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327 </section> |
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328 <output name="logfile" value="TEST_5/TEST_5.log" lines_diff="6"/> |
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329 <output name="summary_txt" value="TEST_5/TEST_5.txt" lines_diff="4"/> |
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330 </test> |
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331 </tests> |
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332 <help><![CDATA[**What it does** |
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333 Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs. |
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334 |
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335 *Comprehensive & taxonomy-independent database* |
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336 Bakta provides a large and taxonomy-independent database using UniProt's entire UniRef protein sequence cluster universe. |
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337 |
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338 *Protein sequence identification* |
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339 Bakta exactly identifies known identical protein sequences (IPS) from RefSeq and UniProt |
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340 allowing the fine-grained annotation of gene alleles (AMR) or closely related but distinct protein families. |
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341 This is achieved via an alignment-free sequence identification (AFSI) approach |
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342 using full-length MD5 protein sequence hash digests. |
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343 *Small proteins/short open reading frames* |
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344 Bakta detects and annotates small proteins/short open reading frames (sORF). |
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345 |
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346 *Expert annotation systems* |
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347 To provide high quality annotations for certain proteins of higher interest, e.g. AMR & VF genes, |
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348 Bakta includes & merges different expert annotation systems. |
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349 Currently, Bakta uses NCBI's AMRFinderPlus for AMR gene annotations |
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350 as well as an generalized protein sequence expert system with distinct |
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351 coverage, identity and priority values for each sequence, currenlty comprising the VFDB as well as NCBI's BlastRules. |
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352 |
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353 *Comprehensive workflow* |
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354 Bakta annotates ncRNA cis-regulatory regions, oriC/oriV/oriT |
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355 and assembly gaps as well as standard feature types: tRNA, tmRNA, rRNA, ncRNA genes, CRISPR, CDS. |
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356 |
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357 *GFF3 & INSDC conform annotations* |
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358 Bakta writes GFF3 and INSDC-compliant (Genbank & EMBL) annotation files ready for submission |
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359 (checked via GenomeTools GFF3Validator, table2asn_GFF and ENA Webin-CLI for GFF3 and EMBL file formats, |
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360 respectively for representative genomes of all ESKAPE species). |
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361 |
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362 *Bacteria & plasmids* |
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363 Bakta was designed to annotate bacteria (isolates & MAGs) and plasmids, only. |
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364 |
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365 **Input options** |
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366 1. Choose a genome or assembly in fasta format to use bakta annotations |
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367 2. Choose A version of the Bakta database |
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368 |
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369 **Organism options** |
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370 You can specify informations about analysed fasta as text input for: |
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371 - genus |
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372 - species |
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373 - strain |
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374 - plasmid |
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375 |
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376 **Annotation options** |
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377 1. You can specify if all sequences (chromosome or plasmids) are complete or not |
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378 2. You can add your own prodigal training file for CDS predictionœ |
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379 3. The translation table could be modified, default is the 11th for bacteria |
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380 4. You can specify if bacteria is gram -/+ or unknonw (default value is unknow) |
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381 5. You can keep the name of contig present in the input file |
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382 6. You can specify your own replicon table as a TSV/CSV file |
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383 7. The compliance option is for ready to submit annotation file to Public database |
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384 as ENA, Genbank EMBL |
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385 8. You can specify a protein sequence file for annotation in GenBank or fasta formats |
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386 Using the Fasta format, each reference sequence can be provided in a short or long format: |
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387 |
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388 # short: |
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389 >id gene~~~product~~~dbxrefs |
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390 MAQ... |
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391 |
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392 # long: |
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393 >id min_identity~~~min_query_cov~~~min_subject_cov~~~gene~~~product~~~dbxrefs |
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394 MAQ... |
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395 |
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396 **Skip steps** |
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397 Some steps could be skiped: |
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398 - skip-trna Skip tRNA detection & annotation |
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399 - skip-tmrna Skip tmRNA detection & annotation |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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400 - skip-rrna Skip rRNA detection & annotation |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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401 - skip-ncrna Skip ncRNA detection & annotation |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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402 - skip-ncrna-region Skip ncRNA region detection & annotation |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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403 - skip-crispr Skip CRISPR array detection & annotation |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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404 - skip-cds Skip CDS detection & annotation |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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405 - skip-pseudo Skip pseudogene detection & annotation |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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406 - skip-sorf Skip sORF detection & annotation |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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407 - skip-gap Skip gap detection & annotation |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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408 - skip-ori Skip oriC/oriT detection & annotation |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
thanhlv
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409 |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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410 **Output options** |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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411 Bakta produce numbers of output files, you can select what type of file you want: |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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412 - Summary of the annotation |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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413 - Annotated files |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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414 - Sequence files for nucleotide and/or amino acid |
54ca20519f70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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415 ]]></help> |
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416 <expand macro="citations"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 6b06711cfba45855d5a992ed1c73c472eaef644f-dirty
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417 </tool> |