From 87968f9a6953ebf322d9fb0fae3a4193b6222288 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Thu, 1 Aug 2024 13:02:23 +0200 Subject: [PATCH] Update tool versions --- .../bacterial-genome-annotation/tutorial.md | 20 ++++++------- .../workflows/Bacterial-Genome-Annotation.ga | 30 +++++++++---------- 2 files changed, 25 insertions(+), 25 deletions(-) diff --git a/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.md b/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.md index bed7dff2d51053..ae2ed5bc0e2ce0 100644 --- a/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.md +++ b/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.md @@ -113,13 +113,13 @@ It is also able to detect and annotate small proteins (sORF). Predicted CDS are > Contig annotation > -> 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` @@ -325,7 +325,7 @@ To detect integrons, we will use **IntegronFinder** ({% cite neron2022integronfi > Integron identification > -> 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` @@ -357,7 +357,7 @@ To detect IS elements, we will use **ISEScan** ({% cite xie2017isescan %}). **IS > IS identification > -> 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} @@ -435,7 +435,7 @@ We would like to look at the annotation using [JBrowse](https://jbrowse.org/jb2/ > Transform PlasmidFinder to GFF > -> 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"* @@ -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` @@ -484,7 +484,7 @@ We would like to look at the annotation using [JBrowse](https://jbrowse.org/jb2/ > 3. Transform to GFF3 > > > Transform IntegronFinder to GFF -> > 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"* @@ -492,7 +492,7 @@ We would like to look at the annotation using [JBrowse](https://jbrowse.org/jb2/ > > - *"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` diff --git a/topics/genome-annotation/tutorials/bacterial-genome-annotation/workflows/Bacterial-Genome-Annotation.ga b/topics/genome-annotation/tutorials/bacterial-genome-annotation/workflows/Bacterial-Genome-Annotation.ga index 0013f19a7eb388..2097f39fcd248c 100644 --- a/topics/genome-annotation/tutorials/bacterial-genome-annotation/workflows/Bacterial-Genome-Annotation.ga +++ b/topics/genome-annotation/tutorials/bacterial-genome-annotation/workflows/Bacterial-Genome-Annotation.ga @@ -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": { @@ -89,7 +89,7 @@ "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", @@ -97,7 +97,7 @@ "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, @@ -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": { @@ -203,7 +203,7 @@ "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", @@ -211,7 +211,7 @@ "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, @@ -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": { @@ -264,7 +264,7 @@ "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", @@ -272,7 +272,7 @@ "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, @@ -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": { @@ -375,7 +375,7 @@ "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", @@ -383,7 +383,7 @@ "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, @@ -391,7 +391,7 @@ }, "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": { @@ -414,7 +414,7 @@ "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", @@ -422,7 +422,7 @@ "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,