Mercurial > repos > iuc > bakta
annotate bakta.xml @ 4:3f0aa1b3e816 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
| author | iuc |
|---|---|
| date | Mon, 24 Jul 2023 11:22:16 +0000 |
| parents | 865ece5ca178 |
| children | 728dacaf08a9 |
| rev | line source |
|---|---|
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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1 <tool id="bakta" name="Bakta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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2 <description> |
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3
865ece5ca178
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
iuc
parents:
2
diff
changeset
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3 Genome annotation via alignment-free sequence identification |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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4 </description> |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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5 <macros> |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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6 <import>macro.xml</import> |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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7 </macros> |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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8 <expand macro='edam'/> |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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9 <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
parents:
diff
changeset
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10 <expand macro="requirements"/> |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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11 <expand macro="version_command"/> |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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12 |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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13 <command detect_errors="aggressive"><![CDATA[ |
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4
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents:
3
diff
changeset
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14 |
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3
865ece5ca178
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
iuc
parents:
2
diff
changeset
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15 mkdir -p ./database_path/amrfinderplus-db && |
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865ece5ca178
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
iuc
parents:
2
diff
changeset
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16 ln -s '$(input_option.bakta_db_select.fields.path)'/* database_path && |
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865ece5ca178
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
iuc
parents:
2
diff
changeset
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17 ln -s '$(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
iuc
parents:
3
diff
changeset
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18 bakta --verbose |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents:
3
diff
changeset
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19 |
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0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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20 #*====================================== |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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21 CPU option |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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22 ======================================*# |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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23 --threads \${GALAXY_SLOTS:-1} |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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24 #*====================================== |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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25 Bakta database |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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26 ======================================*# |
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4
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents:
3
diff
changeset
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27 --db './database_path' |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents:
3
diff
changeset
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28 --output 'bakta_output' |
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0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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29 #if $input_option.min_contig_length |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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30 --min-contig-length $input_option.min_contig_length |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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31 #else if $annotation.compliant |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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32 --min-contig-length 200 |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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33 #else |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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34 --min-contig-length 1 |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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35 #end if |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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36 --prefix bakta_output |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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37 #*====================================== |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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38 Organism options |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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39 genus/species/strain/plasmid |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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40 ======================================*# |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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41 #if $organism.genus |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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42 --genus '$organism.genus' |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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43 #end if |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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44 #if $organism.species |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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45 --species '$organism.species' |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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46 #end if |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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47 #if $organism.strain |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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48 --strain '$organism.strain' |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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49 #end if |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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50 #if $organism.plasmid |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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51 --plasmid '$organism.plasmid' |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
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52 #end if |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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53 #*====================================== |
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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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changeset
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54 Annotation options |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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55 gram type, prodigal/protein file |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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56 ======================================*# |
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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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57 $annotation.complete |
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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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58 #if $annotation.prodigal |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
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59 --prodigal-tf '$annotation.prodigal' |
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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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60 #end if |
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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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61 #if $annotation.translation_table |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
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62 --translation-table '$annotation.translation_table' |
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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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63 #end if |
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3
865ece5ca178
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
iuc
parents:
2
diff
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64 --gram '?' |
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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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65 $annotation.keep_contig_headers |
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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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changeset
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66 #if $annotation.replicons |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
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67 --replicons '$annotation.replicons' |
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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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68 #end if |
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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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69 $annotation.compliant |
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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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70 #if $annotation.proteins |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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71 --proteins '$annotation.proteins' |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
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72 #end if |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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73 #*====================================== |
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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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74 Workflow OPTIONS |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
75 skip some step of the bakta analysis |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
76 ======================================*# |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
77 |
|
2
debdc1469b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
iuc
parents:
1
diff
changeset
|
78 #echo " ".join($workflow.skip_analysis) |
|
0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
79 |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
80 #*====================================== |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
81 Genome file |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
82 ======================================*# |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
83 '$input_option.input_file' |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
84 #*====================================== |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
85 LOG file |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
86 ======================================*# |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
87 | tee '$logfile' |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
88 ]]></command> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
89 <inputs> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
90 <!-- DB and file INPUT --> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
91 <section name="input_option" title="Input/Output options" expanded="true"> |
|
2
debdc1469b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
iuc
parents:
1
diff
changeset
|
92 <param name="bakta_db_select" type="select" label="The bakta database"> |
|
0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
93 <options from_data_table="bakta_database"> |
|
4
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents:
3
diff
changeset
|
94 <filter type="static_value" value="@COMPATIBLE_BAKTA_VERSION@" column="bakta_version"/> |
|
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents:
3
diff
changeset
|
95 <validator message="No bakta database is available" type="no_options"/> |
|
0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
96 </options> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
97 </param> |
|
2
debdc1469b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
iuc
parents:
1
diff
changeset
|
98 <param name="amrfinder_db_select" type="select" label="The amrfinderplus database"> |
|
debdc1469b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
iuc
parents:
1
diff
changeset
|
99 <options from_data_table="amrfinderplus_database"> |
|
debdc1469b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
iuc
parents:
1
diff
changeset
|
100 <validator message="No amrfinderplus database is available" type="no_options"/> |
|
debdc1469b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
iuc
parents:
1
diff
changeset
|
101 </options> |
|
debdc1469b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
iuc
parents:
1
diff
changeset
|
102 </param> |
|
debdc1469b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
iuc
parents:
1
diff
changeset
|
103 |
|
0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
104 <param name="input_file" type="data" format="fasta,fasta.gz" label="Select genome in fasta format"/> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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changeset
|
105 <param name="min_contig_length" type="integer" optional="true" min="0" label="Minimum contig size" help="Minimum contig size (default = 1; 200 in compliant mode) (--min-contig-length)"/> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
106 </section> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
107 <!-- Organism INFORMATION OPTIONS --> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
108 <section name="organism" title="Optional organism options" expanded="false"> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
109 <param argument="--genus" type="text" optional="true" label="Specify genus name" help="ex. Escherichia"> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
110 <validator type="regex">^[a-zA-Z]+$</validator> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
111 </param> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
112 <param argument="--species" type="text" optional="true" label="Specify species name" help="ex. 'coli O157:H7'"> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
113 <validator type="regex">^[a-zA-Z0-9\s(:\-/)]+$</validator> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
114 </param> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
115 <param argument="--strain" type="text" optional="true" label="Specify strain name" help="ex. Sakai"> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
116 <validator type="regex">^[a-zA-Z]+$</validator> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
117 </param> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
118 <param argument="--plasmid" type="text" optional="true" label="Specify plasmid name" help="ex. pOSAK1"> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
119 <validator type="regex">^[a-zA-Z0-9\s(:\-/)]+$</validator> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
120 </param> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
121 </section> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
122 <!-- ANNOTATION --> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
123 <section name="annotation" title="Optional annotation"> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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|
124 <param argument="--complete" type="boolean" truevalue="--complete" falsevalue="" label="Complete replicons" help="All sequences are complete replicons (chromosome/plasmid[s])"/> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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|
125 <param argument="--prodigal" type="data" format="txt" optional="true" label="Prodigal file" help="Prodigal training file for CDS prediction"/> |
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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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changeset
|
126 <param name="translation_table" type="select" optional="true" label="Translation table" help="Default is the bacterial table 11"> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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|
127 <option value="4">4 Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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changeset
|
128 <option value="11" selected="true">11 Bacterial, Archaeal and Plant Plastid Code</option> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
129 </param> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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|
130 <param name="keep_contig_headers" type="boolean" truevalue="--keep-contig-headers" falsevalue="" label="Keep original contig header (--keep-contig-headers)"/> |
|
3
865ece5ca178
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
iuc
parents:
2
diff
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|
131 <param argument="--replicons" type="data" format="tabular,csv" optional="true" label="Replicon information table (tsv/csv)" help=""/> |
|
0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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|
132 <param argument="--compliant" type="boolean" truevalue="--compliant" falsevalue="" label="Force Genbank/ENA/DDJB compliance"/> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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|
133 <param argument="--proteins" type="data" format="fasta" optional="true" label="Protein fasta file" help="Fasta file of trusted protein sequences for CDS annotation"/> |
|
4
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents:
3
diff
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134 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" label="Metagenome mode" help="Run in metagenome mode. This only affects CDS prediction"/> |
|
0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
135 </section> |
|
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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changeset
|
136 <!-- PARAMETER FOR WORKFLOW ANALYSIS --> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
137 <section name="workflow" title="Workflow option to skip steps"> |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
138 <param name="skip_analysis" type="select" display="checkboxes" multiple="true" label="Select steps to skip"> |
|
4
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents:
3
diff
changeset
|
139 <option value="--skip-trna">Skip tRNA detection and annotation</option> |
|
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents:
3
diff
changeset
|
140 <option value="--skip-tmrna">Skip tmRNA detection and annotation</option> |
|
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents:
3
diff
changeset
|
141 <option value="--skip-rrna">Skip rRNA detection and annotation</option> |
|
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents:
3
diff
changeset
|
142 <option value="--skip-ncrna">Skip ncRNA detection and annotation</option> |
|
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents:
3
diff
changeset
|
143 <option value="--skip-ncrna-region">Skip ncRNA region detection and annotation</option> |
|
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents:
3
diff
changeset
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144 <option value="--skip-crispr">Skip CRISPR array detection and annotation</option> |
|
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
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diff
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145 <option value="--skip-cds">Skip CDS detection and annotation</option> |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents:
3
diff
changeset
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146 <option value="--skip-pseudo">Skip pseudogene detection and annotation</option> |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents:
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diff
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147 <option value="--skip-sorf">Skip sORF detection and annotation</option> |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
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148 <option value="--skip-gap">Skip gap detection and annotation</option> |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents:
3
diff
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149 <option value="--skip-ori">Skip oriC/oriT detection and annotation</option> |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents:
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diff
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150 <option value="--skip-plot">Skip generation of circular genome plots</option> |
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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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changeset
|
151 </param> |
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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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changeset
|
152 </section> |
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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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changeset
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153 <section name="output_files" title="Selection of the output files"> |
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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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154 <param name="output_selection" type="select" display="checkboxes" multiple="true" label="Output files selection"> |
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4
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents:
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diff
changeset
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155 <option value="file_tsv" selected="true">Annotation file in TSV</option> |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents:
3
diff
changeset
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156 <option value="file_gff3" selected="true">Annotation and sequence in GFF3</option> |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents:
3
diff
changeset
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157 <option value="file_gbff" selected="false">Annotations and sequences in GenBank format</option> |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
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3
diff
changeset
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158 <option value="file_embl" selected="false">Annotations and sequences in EMBL format</option> |
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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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diff
changeset
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159 <option value="file_fna" selected="false">Replicon/contig DNA sequences as FASTA</option> |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
parents:
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diff
changeset
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160 <option value="file_ffn" selected="true">Feature nucleotide sequences as FASTA</option> |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
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diff
changeset
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161 <option value="file_faa" selected="false">CDS/sORF amino acid sequences as FASTA</option> |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
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3
diff
changeset
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162 <option value="hypo_tsv" selected="false">Hypothetical protein CDS in TSV</option> |
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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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diff
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163 <option value="hypo_fa" selected="false">Hypothetical protein CDS amino sequences as FASTA</option> |
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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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164 <option value="sum_txt" selected="false">Summary as TXT</option> |
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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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diff
changeset
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165 <option value="file_json" selected="false">Information on each annotated feature as JSON</option> |
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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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166 <option value="file_plot" selected="true">Plot of the annotation result as SVG</option> |
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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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167 <option value="log_txt" selected="false">Log file as TXT</option> |
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0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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changeset
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168 </param> |
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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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169 </section> |
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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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170 |
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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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171 </inputs> |
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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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172 <outputs> |
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4
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
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173 <data name="annotation_tsv" format="tabular" from_work_dir="bakta_output/bakta_output.tsv" label="${tool.name} on ${on_string}: annotation_summary"> |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
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174 <filter>output_files['output_selection'] and "file_tsv" in output_files['output_selection']</filter> |
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0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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changeset
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175 </data> |
|
4
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
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176 <data name="annotation_gff3" format="gff3" from_work_dir="bakta_output/bakta_output.gff3" label="${tool.name} on ${on_string}: Annotation_and_sequences"> |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
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177 <filter>output_files['output_selection'] and "file_gff3" in output_files['output_selection']</filter> |
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0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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178 </data> |
|
4
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
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179 <data name="annotation_gbff" format="tabular" from_work_dir="bakta_output/bakta_output.gbff" label="${tool.name} on ${on_string}: bakta_output.gbff"> |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
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180 <filter>output_files['output_selection'] and "file_gbff" in output_files['output_selection']</filter> |
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0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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181 </data> |
|
4
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
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182 <data name="annotation_embl" format="tabular" from_work_dir="bakta_output/bakta_output.embl" label="${tool.name} on ${on_string}: bakta_output.embl"> |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
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diff
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183 <filter>output_files['output_selection'] and "file_embl" in output_files['output_selection']</filter> |
|
0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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changeset
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184 </data> |
|
4
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
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diff
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185 <data name="annotation_fna" format="fasta" from_work_dir="bakta_output/bakta_output.fna" label="${tool.name} on ${on_string}: Contig_sequences"> |
|
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
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diff
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186 <filter>output_files['output_selection'] and "file_fna" in output_files['output_selection']</filter> |
|
0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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187 </data> |
|
4
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
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188 <data name="annotation_ffn" format="fasta" from_work_dir="bakta_output/bakta_output.ffn" label="${tool.name} on ${on_string}: Nucleotide_sequences"> |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
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189 <filter>output_files['output_selection'] and "file_ffn" in output_files['output_selection']</filter> |
|
0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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changeset
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190 </data> |
|
4
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
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diff
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191 <data name="annotation_faa" format="fasta" from_work_dir="bakta_output/bakta_output.faa" label="${tool.name} on ${on_string}: Amino_acid_sequences"> |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
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diff
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192 <filter>output_files['output_selection'] and "file_faa" in output_files['output_selection']</filter> |
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0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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changeset
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193 </data> |
|
4
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
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194 <data name="hypotheticals_tsv" format="tabular" from_work_dir="bakta_output/bakta_output.hypotheticals.tsv" label="${tool.name} on ${on_string}: hypothetical_annotation_summary"> |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
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195 <filter>output_files['output_selection'] and "hypo_tsv" in output_files['output_selection']</filter> |
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0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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196 </data> |
|
4
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
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197 <data name="hypotheticals_faa" format="fasta" from_work_dir="bakta_output/bakta_output.hypotheticals.faa" label="${tool.name} on ${on_string}: hypothetical_amino_acid_sequences"> |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
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198 <filter>output_files['output_selection'] and "hypo_fa" in output_files['output_selection']</filter> |
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0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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199 </data> |
|
4
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
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200 <data name="summary_txt" format="txt" from_work_dir="bakta_output/bakta_output.txt" label="${tool.name} on ${on_string}: Analysis_summary"> |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
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201 <filter>output_files['output_selection'] and "sum_txt" in output_files['output_selection']</filter> |
|
0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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202 </data> |
|
4
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
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203 <data name="annotation_json" format="json" from_work_dir="bakta_output/bakta_output.json" label="${tool.name} on ${on_string}: annotation_machine_readable"> |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
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204 <filter>output_files['output_selection'] and "file_json" in output_files['output_selection']</filter> |
|
0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
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changeset
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205 </data> |
|
4
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
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206 <data name="annotation_plot" format="svg" from_work_dir="bakta_output/bakta_output.svg" label="${tool.name} on ${on_string}: Plot of the annotation"> |
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3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
iuc
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207 <filter>output_files['output_selection'] and "file_plot" in output_files['output_selection']</filter> |
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2
debdc1469b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
iuc
parents:
1
diff
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208 </data> |
|
0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
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209 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file"> |
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4
3f0aa1b3e816
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit e2c4ab5546b135ff903545073c3223aab166d8f5
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210 <filter>output_files['output_selection'] and "log_txt" in output_files['output_selection']</filter> |
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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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211 </data> |
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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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212 </outputs> |
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213 <tests> |
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214 <test expect_num_outputs="13"> <!-- TEST_1 database + input --> |
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215 <section name="input_option" > |
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216 <param name="bakta_db_select" value="V5.0_2022-08-19"/> |
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217 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> |
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218 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/> |
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219 <param name="min_contig_length" value="250"/> |
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220 </section> |
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221 <section name="output_files"> |
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222 <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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
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223 </section> |
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224 <output name="annotation_tsv" value="TEST_1/TEST_1.tsv" lines_diff="2"/> |
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225 <output name="annotation_gff3" value="TEST_1/TEST_1.gff3" lines_diff="2"/> |
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226 <output name="annotation_gbff" value="TEST_1/TEST_1.gbff" lines_diff="8"/> |
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227 <output name="annotation_embl" value="TEST_1/TEST_1.embl" lines_diff="6"/> |
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228 <output name="annotation_fna" value="TEST_1/TEST_1.fna"/> |
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229 <output name="annotation_ffn" value="TEST_1/TEST_1.ffn"/> |
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230 <output name="annotation_faa" value="TEST_1/TEST_1.faa"/> |
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231 <output name="hypotheticals_tsv" value="TEST_1/TEST_1.hypotheticals.tsv" lines_diff="4"/> |
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232 <output name="hypotheticals_faa" value="TEST_1/TEST_1.hypotheticals.faa"/> |
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233 <output name="summary_txt" value="TEST_1/TEST_1.txt" lines_diff="4"/> |
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234 <output name="annotation_plot" value="TEST_1/TEST_1_plot.svg" ftype="svg" compare="sim_size"/> |
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235 <output name="annotation_json" value="TEST_1/TEST_1.json" lines_diff="6"/> |
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236 <output name="logfile" value="TEST_1/TEST_1.log" lines_diff="15"/> |
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237 </test> |
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238 <test expect_num_outputs="4"> <!-- TEST_2 another input, add organism info some annotations and skip 2 steps --> |
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239 <section name="input_option" > |
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240 <param name="bakta_db_select" value="V5.0_2022-08-19"/> |
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241 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> |
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242 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/> |
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243 <param name="min_contig_length" value="250"/> |
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244 </section> |
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245 <section name="organism"> |
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246 <param name="genus" value="Escherichia"/> |
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247 <param name="species" value="coli O157:H7"/> |
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248 <param name="strain" value="Sakai"/> |
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249 <param name="plasmid" value="pOSAK1"/> |
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250 </section> |
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251 <section name="annotation"> |
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252 <param name="keep_contig_headers" value="true"/> |
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253 </section> |
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254 <section name="workflow"> |
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255 <param name="skip_analysis" value="--skip-trna,--skip-tmrna"/> |
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256 </section> |
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257 <output name="annotation_tsv" value="TEST_2/TEST_2.tsv" lines_diff="4"> |
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258 <assert_contents> |
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259 <has_text_matching expression="IHHALP_00005"/> |
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260 </assert_contents> |
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261 </output> |
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262 <output name="annotation_gff3" value="TEST_2/TEST_2.gff3" lines_diff="4"> |
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263 <assert_contents> |
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264 <has_text_matching expression="ID=NC_002127.1;Name=NC_002127.1;Is_circular=true"/> |
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265 </assert_contents> |
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266 </output> |
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267 <output name="annotation_ffn" value="TEST_2/TEST_2.ffn"/> |
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268 <output name="annotation_plot" value="TEST_2/TEST_2_plot.svg" ftype="svg" compare="sim_size"/> |
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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="V5.0_2022-08-19"/> |
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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,--skip-plot"/> |
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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 </test> |
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284 <test expect_num_outputs="4"> <!-- TEST_4 annotations --> |
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285 <section name="input_option" > |
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286 <param name="bakta_db_select" value="V5.0_2022-08-19"/> |
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287 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> |
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288 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/> |
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289 </section> |
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290 <section name="annotation"> |
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291 <param name="complete" value="true"/> |
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292 <param name="prodigal" value="prodigal.tf"/> |
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293 <param name="translation_table" value="4"/> |
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294 <param name="replicons" value="replicons.tsv" ftype="tabular"/> |
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295 <param name="compliant" value="true"/> |
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296 <param name="proteins" value="user-proteins.faa" ftype="fasta"/> |
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297 </section> |
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298 <output name="annotation_tsv" value="TEST_4/TEST_4.tsv" lines_diff="4"/> |
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299 <output name="annotation_gff3" value="TEST_4/TEST_4.gff3" lines_diff="4"/> |
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300 <output name="annotation_ffn" value="TEST_4/TEST_4.ffn"/> |
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301 <output name="annotation_plot" value="TEST_4/TEST_4_plot.svg" ftype="svg" compare="sim_size"/> |
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302 </test> |
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303 <test expect_num_outputs="2"> <!-- TEST_5 skip all steps and keep only the logfile and summary --> |
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304 <section name="input_option" > |
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305 <param name="bakta_db_select" value="V5.0_2022-08-19"/> |
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306 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> |
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307 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/> |
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308 </section> |
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309 <section name="annotation"> |
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310 <param name="complete" value="true"/> |
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311 <param name="translation_table" value="4"/> |
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312 </section> |
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313 <section name="workflow"> |
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314 <param name="skip_analysis" value="--skip-trna,--skip-tmrna,--skip-rrna,--skip-ncrna,--skip-ncrna-region,--skip-crispr,--skip-cds,--skip-sorf,--skip-gap,--skip-ori,--skip-plot"/> |
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315 </section> |
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316 <section name="output_files"> |
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317 <param name="output_selection" value="log_txt,sum_txt"/> |
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318 </section> |
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319 <output name="logfile" value="TEST_5/TEST_5.log" lines_diff="13"/> |
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320 <output name="summary_txt" value="TEST_5/TEST_5.txt" lines_diff="4"/> |
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321 </test> |
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322 <test expect_num_outputs="13"> <!-- TEST_6 metagenome option --> |
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323 <section name="input_option" > |
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324 <param name="bakta_db_select" value="V5.0_2022-08-19"/> |
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325 <param name="amrfinder_db_select" value="V3.6-2020-03-20.1"/> |
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326 <param name="input_file" value="NC_002127.1.fna" ftype="fasta"/> |
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327 </section> |
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328 <section name="annotation"> |
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329 <param name="meta" value="true"/> |
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330 </section> |
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331 <section name="output_files"> |
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332 <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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333 </section> |
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334 <output name="annotation_tsv" value="TEST_6/TEST_6.tsv" lines_diff="2"/> |
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335 <output name="annotation_gff3" value="TEST_6/TEST_6.gff3" lines_diff="2"/> |
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336 <output name="annotation_gbff" value="TEST_6/TEST_6.gbff" lines_diff="8"/> |
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337 <output name="annotation_embl" value="TEST_6/TEST_6.embl" lines_diff="6"/> |
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338 <output name="annotation_fna" value="TEST_6/TEST_6.fna"/> |
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339 <output name="annotation_ffn" value="TEST_6/TEST_6.ffn"/> |
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340 <output name="annotation_faa" value="TEST_6/TEST_6.faa"/> |
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341 <output name="hypotheticals_tsv" value="TEST_6/TEST_6.hypotheticals.tsv" lines_diff="4"/> |
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342 <output name="hypotheticals_faa" value="TEST_6/TEST_6.hypotheticals.faa"/> |
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343 <output name="summary_txt" value="TEST_6/TEST_6.txt" lines_diff="4"/> |
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344 <output name="annotation_plot" value="TEST_6/TEST_6_plot.svg" ftype="svg" compare="sim_size"/> |
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345 <output name="annotation_json" value="TEST_6/TEST_6.json" lines_diff="6"/> |
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346 <output name="logfile" value="TEST_6/TEST_6.log" lines_diff="15"/> |
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347 </test> |
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348 </tests> |
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349 <help><![CDATA[**What it does** |
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350 Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs. |
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351 |
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352 *Comprehensive & taxonomy-independent database* |
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353 Bakta provides a large and taxonomy-independent database using UniProt's entire UniRef protein sequence cluster universe. |
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354 |
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355 *Protein sequence identification* |
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356 Bakta exactly identifies known identical protein sequences (IPS) from RefSeq and UniProt |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
357 allowing the fine-grained annotation of gene alleles (AMR) or closely related but distinct protein families. |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
358 This is achieved via an alignment-free sequence identification (AFSI) approach |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
359 using full-length MD5 protein sequence hash digests. |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
360 *Small proteins/short open reading frames* |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
361 Bakta detects and annotates small proteins/short open reading frames (sORF). |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
362 |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
363 *Expert annotation systems* |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
364 To provide high quality annotations for certain proteins of higher interest, e.g. AMR & VF genes, |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
365 Bakta includes & merges different expert annotation systems. |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
366 Currently, Bakta uses NCBI's AMRFinderPlus for AMR gene annotations |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
367 as well as an generalized protein sequence expert system with distinct |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
368 coverage, identity and priority values for each sequence, currenlty comprising the VFDB as well as NCBI's BlastRules. |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
369 |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
370 *Comprehensive workflow* |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
371 Bakta annotates ncRNA cis-regulatory regions, oriC/oriV/oriT |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
372 and assembly gaps as well as standard feature types: tRNA, tmRNA, rRNA, ncRNA genes, CRISPR, CDS. |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
373 |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
374 *GFF3 & INSDC conform annotations* |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
375 Bakta writes GFF3 and INSDC-compliant (Genbank & EMBL) annotation files ready for submission |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
376 (checked via GenomeTools GFF3Validator, table2asn_GFF and ENA Webin-CLI for GFF3 and EMBL file formats, |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
377 respectively for representative genomes of all ESKAPE species). |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
378 |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
379 *Bacteria & plasmids* |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
380 Bakta was designed to annotate bacteria (isolates & MAGs) and plasmids, only. |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
381 |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
382 **Input options** |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
383 1. Choose a genome or assembly in fasta format to use bakta annotations |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
384 2. Choose A version of the Bakta database |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
385 |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
386 **Organism options** |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
387 You can specify informations about analysed fasta as text input for: |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
388 - genus |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
389 - species |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
390 - strain |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
391 - plasmid |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
392 |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
393 **Annotation options** |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
394 1. You can specify if all sequences (chromosome or plasmids) are complete or not |
|
2
debdc1469b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 74f8fe2e7de713920026d372b28c73adb04ee97c
iuc
parents:
1
diff
changeset
|
395 2. You can add your own prodigal training file for CDS predictionœ |
|
0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
396 3. The translation table could be modified, default is the 11th for bacteria |
|
3
865ece5ca178
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit 9f516ce5c84b251b9041cd79129e5b5e1979a738
iuc
parents:
2
diff
changeset
|
397 4. You can specify if bacteria is gram -/+ or unknonw (default value is unknow) |
|
0
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
398 5. You can keep the name of contig present in the input file |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
399 6. You can specify your own replicon table as a TSV/CSV file |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
400 7. The compliance option is for ready to submit annotation file to Public database |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
401 as ENA, Genbank EMBL |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
402 8. You can specify a protein sequence file for annotation in GenBank or fasta formats |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
403 Using the Fasta format, each reference sequence can be provided in a short or long format: |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
404 |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
405 # short: |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
406 >id gene~~~product~~~dbxrefs |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
407 MAQ... |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
408 |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
409 # long: |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
410 >id min_identity~~~min_query_cov~~~min_subject_cov~~~gene~~~product~~~dbxrefs |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
411 MAQ... |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
412 |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
413 **Skip steps** |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
414 Some steps could be skiped: |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
415 - skip-trna Skip tRNA detection & annotation |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
416 - skip-tmrna Skip tmRNA detection & annotation |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
417 - skip-rrna Skip rRNA detection & annotation |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
418 - skip-ncrna Skip ncRNA detection & annotation |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
419 - skip-ncrna-region Skip ncRNA region detection & annotation |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
420 - skip-crispr Skip CRISPR array detection & annotation |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
421 - skip-cds Skip CDS detection & annotation |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
422 - skip-pseudo Skip pseudogene detection & annotation |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
423 - skip-sorf Skip sORF detection & annotation |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
424 - skip-gap Skip gap detection & annotation |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
425 - skip-ori Skip oriC/oriT detection & annotation |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
426 |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
427 **Output options** |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
428 Bakta produce numbers of output files, you can select what type of file you want: |
|
1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
429 - Summary of the annotation |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
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430 - Annotated files |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
431 - Sequence files for nucleotide and/or amino acid |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
432 ]]></help> |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
433 <expand macro="citations"/> |
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1a27ad3d0cdf
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit 7d595b05b8d595f554b57dadbf1beb0b39733af3
iuc
parents:
diff
changeset
|
434 </tool> |