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Merge pull request #5192 from galaxyproject/bacterial-genome-annotati…
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…on-bakta-update

[Bacterial Genome Annotation] Update tool versions
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@bebatut
bebatut authored Aug 1, 2024
2 parents 1d5f31c + 5cd92b4 commit 4ee0cef
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20 changes: 10 additions & 10 deletions topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.md
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Expand Up @@ -113,13 +113,13 @@ It is also able to detect and annotate small proteins (sORF). Predicted CDS are
> <hands-on-title>Contig annotation</hands-on-title>
>
> 1. {% tool [Bakta](toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.2+galaxy0) %} with the following parameters:
> 1. {% tool [Bakta](toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0) %} with the following parameters:
> - In *"Input/Output options"*:
> - *"The bakta database"*: latest one
> - *"The amrfinderplus database"*: latest one
> - {% icon param-file %} *"Select genome in fasta format"*: Contig file
> - *"Bakta database"*: latest one
> - *"AMRFinderPlus database"*: latest one
> - In *"Optional annotation"*:
> - *"Keep original contig header (--keep-contig-headers)"*: `Yes`
> - *"Keep original contig header"*: `Yes`
> - In *"Selection of the output files"*:
> - *"Output files selection"*:
> - `Annotation file in TSV`
Expand Down Expand Up @@ -325,7 +325,7 @@ To detect integrons, we will use **IntegronFinder** ({% cite neron2022integronfi
> <hands-on-title> Integron identification</hands-on-title>
>
> 1. {% tool [IntegronFinder](toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.2+galaxy1) %} with the following parameters:
> 1. {% tool [IntegronFinder](toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0) %} with the following parameters:
> - {% icon param-file %} *"Replicon file"*: Contig file
> - *"Thorough local detection"*: `Yes`
> - *"Search also for promoter and attI sites?"*: `Yes`
Expand Down Expand Up @@ -357,7 +357,7 @@ To detect IS elements, we will use **ISEScan** ({% cite xie2017isescan %}). **IS
> <hands-on-title> IS identification </hands-on-title>
>
> 1. {% tool [ISEScan](toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy0) %} with the following parameters:
> 1. {% tool [ISEScan](toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1) %} with the following parameters:
> - {% icon param-file %} *"Genome fasta input"*: Contig file
>
{: .hands_on}
Expand Down Expand Up @@ -435,7 +435,7 @@ We would like to look at the annotation using [JBrowse](https://jbrowse.org/jb2/
> <hands-on-title> Transform PlasmidFinder to GFF </hands-on-title>
>
> 1. {% tool [Replace Text in a specific column](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3) %} with the following parameters:
> 1. {% tool [Replace Text in a specific column](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1) %} with the following parameters:
> - {% icon param-file %} *"File to process"*: `results.tsv` output of **PlasmidFinder**
> - In *"Replacement"*:
> - In *"1: Replacement"*
Expand All @@ -453,7 +453,7 @@ We would like to look at the annotation using [JBrowse](https://jbrowse.org/jb2/
>
> This will remove in the content of column 5 what is after the contig name
>
> 2. {% tool [Select last lines from a dataset](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0) %} with the following parameters:
> 2. {% tool [Select last lines from a dataset](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1) %} with the following parameters:
> - {% icon param-file %} *"Text file"*: output of **Replace Text** above
> - *"Operation"*: `Keep everything from this line on`
> - *"Number of lines"*: `2`
Expand Down Expand Up @@ -484,15 +484,15 @@ We would like to look at the annotation using [JBrowse](https://jbrowse.org/jb2/
> 3. Transform to GFF3
>
> > <hands-on-title> Transform IntegronFinder to GFF </hands-on-title>
> > 1. {% tool [Replace Text in a specific column](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3) %} with the following parameters:
> > 1. {% tool [Replace Text in a specific column](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1) %} with the following parameters:
> > - {% icon param-file %} *"File to process"*: tabular output of **IntegronFinder**
> > - In *"Replacement"*:
> > - In *"1: Replacement"*
> > - *in column*: `Column: 7`
> > - *"Find pattern"*: `NA`
> > - *"Replace with"*: `0`
> >
> > 2. {% tool [Select last lines from a dataset](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0) %} with the following parameters:
> > 2. {% tool [Select last lines from a dataset](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1) %} with the following parameters:
> > - {% icon param-file %} *"Text file"*: output of **Replace Text** above
> > - *"Operation"*: `Keep everything from this line on`
> > - *"Number of lines"*: `3`
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30 changes: 15 additions & 15 deletions ...annotation/tutorials/bacterial-genome-annotation/workflows/Bacterial-Genome-Annotation.ga
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Expand Up @@ -46,7 +46,7 @@
},
"1": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy0",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1",
"errors": null,
"id": 1,
"input_connections": {
Expand Down Expand Up @@ -89,15 +89,15 @@
"top": 133
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "19f42b3ea391",
"name": "isescan",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"log_activate\": false, \"remove_short_is\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.7.2.3+galaxy0",
"tool_version": "1.7.2.3+galaxy1",
"type": "tool",
"uuid": "334b327f-be00-4e75-ae01-c3ba674dbc9b",
"when": null,
Expand Down Expand Up @@ -168,7 +168,7 @@
},
"3": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.2+galaxy1",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0",
"errors": null,
"id": 3,
"input_connections": {
Expand Down Expand Up @@ -203,15 +203,15 @@
"output_name": "integrons_table"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.2+galaxy1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0",
"tool_shed_repository": {
"changeset_revision": "4768f7f8e93f",
"name": "integron_finder",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"gbk\": false, \"local_max\": true, \"no_logfile\": true, \"pdf\": false, \"promoter_attI\": true, \"sequence\": {\"__class__\": \"ConnectedValue\"}, \"settings\": {\"attc_settings\": {\"dist_thresh\": \"4000\", \"calin_threshold\": \"2\", \"max_attc_size\": \"200\", \"min_attc_size\": \"40\", \"keep_palindromes\": false, \"covar_matrix\": null}, \"protein_settings\": {\"no_proteins\": false, \"union_integrases\": false, \"func_annot\": false}}, \"topology_file\": null, \"type_replicon\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.0.2+galaxy1",
"tool_version": "2.0.5+galaxy0",
"type": "tool",
"uuid": "29a9252c-5c3b-4024-99ff-637d0572320a",
"when": null,
Expand All @@ -225,7 +225,7 @@
},
"4": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.2+galaxy0",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0",
"errors": null,
"id": 4,
"input_connections": {
Expand Down Expand Up @@ -264,15 +264,15 @@
"top": 0
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.2+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0",
"tool_shed_repository": {
"changeset_revision": "728dacaf08a9",
"name": "bakta",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__input_ext\": \"input\", \"annotation\": {\"complete\": false, \"prodigal\": null, \"translation_table\": \"11\", \"keep_contig_headers\": true, \"replicons\": null, \"compliant\": false, \"proteins\": null, \"meta\": false}, \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input_option\": {\"bakta_db_select\": \"V5.0_2023-02-20\", \"amrfinder_db_select\": \"amrfinderplus_V3.11_2022-12-19.1\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"min_contig_length\": null}, \"organism\": {\"genus\": null, \"species\": null, \"strain\": null, \"plasmid\": null}, \"output_files\": {\"output_selection\": [\"file_tsv\", \"file_gff3\", \"file_ffn\", \"file_plot\", \"sum_txt\"]}, \"workflow\": {\"skip_analysis\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.8.2+galaxy0",
"tool_version": "1.9.3+galaxy0",
"type": "tool",
"uuid": "181220e7-9082-48bc-b855-f10baf78fc2a",
"when": null,
Expand Down Expand Up @@ -352,7 +352,7 @@
},
"7": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1",
"errors": null,
"id": 7,
"input_connections": {
Expand All @@ -375,23 +375,23 @@
"top": 465
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "ddf54b12c295",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"replacements\": [{\"__index__\": 0, \"column\": \"6\", \"find_pattern\": \"(.*)\\\\.\\\\.(.*)\", \"replace_pattern\": \"\\\\\\\\1\\\\t\\\\\\\\2\"}, {\"__index__\": 1, \"column\": \"5\", \"find_pattern\": \"(.*)( len.*)\", \"replace_pattern\": \"\\\\\\\\1\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.1.3",
"tool_version": "9.3+galaxy1",
"type": "tool",
"uuid": "0dc6507b-6e6c-4edc-bd4a-9ffb5bae5a55",
"when": null,
"workflow_outputs": []
},
"8": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1",
"errors": null,
"id": 8,
"input_connections": {
Expand All @@ -414,15 +414,15 @@
"top": 465
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "ddf54b12c295",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"complement\": \"+\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"num_lines\": \"2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.1.0",
"tool_version": "9.3+galaxy1",
"type": "tool",
"uuid": "cd3e0f3d-66f5-47a3-bd55-c4a5cc474d97",
"when": null,
Expand Down

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