From ed3325d60843b30358cdb704f83ad9ea4b6c149f Mon Sep 17 00:00:00 2001 From: Anthony Bretaudeau Date: Wed, 26 Apr 2023 16:23:27 +0200 Subject: [PATCH] update funannotate tuto --- .../tutorials/funannotate/data-library.yaml | 26 +- .../tutorials/funannotate/tutorial.md | 62 +- .../workflows/funannotate-tests.yml | 12 +- .../{main_workflow.ga => funannotate.ga} | 556 ++++++------------ .../tutorials/functional/content.md | 4 +- .../functional/workflows/functional-tests.yml | 2 +- .../functional/workflows/main_workflow.ga | 14 +- 7 files changed, 218 insertions(+), 458 deletions(-) rename topics/genome-annotation/tutorials/funannotate/workflows/{main_workflow.ga => funannotate.ga} (69%) diff --git a/topics/genome-annotation/tutorials/funannotate/data-library.yaml b/topics/genome-annotation/tutorials/funannotate/data-library.yaml index 2441261b716643..edb3059e490a7c 100644 --- a/topics/genome-annotation/tutorials/funannotate/data-library.yaml +++ b/topics/genome-annotation/tutorials/funannotate/data-library.yaml @@ -10,30 +10,30 @@ items: items: - name: Genome annotation with Funannotate items: - - name: 'DOI: 10.5281/zenodo.5906635' + - name: 'DOI: 10.5281/zenodo.7867921' description: latest items: - - url: https://zenodo.org/api/files/8c2cc766-2b68-45bd-a2d3-391acf9bdb1b/alternate_annotation.gbk + - url: https://zenodo.org/api/files/47406781-e8af-42e7-855d-d29e4a098f6f/alternate_annotation.gbk src: url ext: genbank - info: https://zenodo.org/record/5906635 - - url: https://zenodo.org/api/files/8c2cc766-2b68-45bd-a2d3-391acf9bdb1b/alternate_annotation.gff3 + info: https://zenodo.org/record/7867921 + - url: https://zenodo.org/api/files/47406781-e8af-42e7-855d-d29e4a098f6f/alternate_annotation.gff3 src: url ext: gff3 - info: https://zenodo.org/record/5906635 - - url: https://zenodo.org/api/files/8c2cc766-2b68-45bd-a2d3-391acf9bdb1b/genome_masked.fasta + info: https://zenodo.org/record/7867921 + - url: https://zenodo.org/api/files/47406781-e8af-42e7-855d-d29e4a098f6f/genome_masked.fasta src: url ext: fasta - info: https://zenodo.org/record/5906635 - - url: https://zenodo.org/api/files/8c2cc766-2b68-45bd-a2d3-391acf9bdb1b/rnaseq_R1.fq.gz + info: https://zenodo.org/record/7867921 + - url: https://zenodo.org/api/files/47406781-e8af-42e7-855d-d29e4a098f6f/rnaseq_R1.fq.gz src: url ext: fastqsanger.gz - info: https://zenodo.org/record/5906635 - - url: https://zenodo.org/api/files/8c2cc766-2b68-45bd-a2d3-391acf9bdb1b/rnaseq_R2.fq.gz + info: https://zenodo.org/record/7867921 + - url: https://zenodo.org/api/files/47406781-e8af-42e7-855d-d29e4a098f6f/rnaseq_R2.fq.gz src: url ext: fastqsanger.gz - info: https://zenodo.org/record/5906635 - - url: https://zenodo.org/api/files/8c2cc766-2b68-45bd-a2d3-391acf9bdb1b/SwissProt_subset.fasta + info: https://zenodo.org/record/7867921 + - url: https://zenodo.org/api/files/47406781-e8af-42e7-855d-d29e4a098f6f/SwissProt_subset.fasta src: url ext: fasta - info: https://zenodo.org/record/5906635 + info: https://zenodo.org/record/7867921 diff --git a/topics/genome-annotation/tutorials/funannotate/tutorial.md b/topics/genome-annotation/tutorials/funannotate/tutorial.md index 3397922b34134e..49f156b2420302 100644 --- a/topics/genome-annotation/tutorials/funannotate/tutorial.md +++ b/topics/genome-annotation/tutorials/funannotate/tutorial.md @@ -2,7 +2,7 @@ layout: tutorial_hands_on title: Genome annotation with Funannotate -zenodo_link: https://zenodo.org/record/5726818 +zenodo_link: https://zenodo.org/record/7867921 tags: - eukaryote questions: @@ -95,12 +95,12 @@ To annotate our genome using Funannotate, we will use the following files: > -> `{{ page.title }}`): > > ``` -> https://zenodo.org/api/files/8c2cc766-2b68-45bd-a2d3-391acf9bdb1b/genome_masked.fasta -> https://zenodo.org/api/files/8c2cc766-2b68-45bd-a2d3-391acf9bdb1b/rnaseq_R1.fq.gz -> https://zenodo.org/api/files/8c2cc766-2b68-45bd-a2d3-391acf9bdb1b/rnaseq_R2.fq.gz -> https://zenodo.org/api/files/8c2cc766-2b68-45bd-a2d3-391acf9bdb1b/SwissProt_subset.fasta -> https://zenodo.org/api/files/8c2cc766-2b68-45bd-a2d3-391acf9bdb1b/alternate_annotation.gbk -> https://zenodo.org/api/files/8c2cc766-2b68-45bd-a2d3-391acf9bdb1b/alternate_annotation.gff3 +> https://zenodo.org/api/files/47406781-e8af-42e7-855d-d29e4a098f6f/genome_masked.fasta +> https://zenodo.org/api/files/47406781-e8af-42e7-855d-d29e4a098f6f/rnaseq_R1.fq.gz +> https://zenodo.org/api/files/47406781-e8af-42e7-855d-d29e4a098f6f/rnaseq_R2.fq.gz +> https://zenodo.org/api/files/47406781-e8af-42e7-855d-d29e4a098f6f/SwissProt_subset.fasta +> https://zenodo.org/api/files/47406781-e8af-42e7-855d-d29e4a098f6f/alternate_annotation.gbk +> https://zenodo.org/api/files/47406781-e8af-42e7-855d-d29e4a098f6f/alternate_annotation.gff3 > ``` > > {% snippet faqs/galaxy/datasets_import_via_link.md %} @@ -108,40 +108,6 @@ To annotate our genome using Funannotate, we will use the following files: > {: .hands_on} -# Preparing the genome sequence - -Before annotating the genome, we want to make sure that the fasta file is properly formatted. We do it now to make sure we will not encounter unexpected errors later in the annotation process. - -Funannotate provides two little tools to help us. Let's run the two tools, one after the other. - -The first one ({% tool [Funannotate assembly clean](toolshed.g2.bx.psu.edu/repos/iuc/funannotate_clean/funannotate_clean/1.8.9+galaxy2) %}) compares all the sequences between them, and removes the shorter ones that are already included in longer ones. This is to reduce unexpected redundancy in the genome. This step is recommended only for haploid genomes (we know our organism is haploid). This first tool also removes any suspicious sequence (like sequences made only of 1 or 2 letters, instead of the 5 expected (ATGCN). - -The second tool will ensure that our fasta file is sorted, based on the length of the contigs (the longest ones first). It will also rename contigs to make sure the name are standard (they will all begin with `scaffold_`, then a number). - -> Polish the assembly -> -> 1. {% tool [Funannotate assembly clean](toolshed.g2.bx.psu.edu/repos/iuc/funannotate_clean/funannotate_clean/1.8.9+galaxy2) %} with the following parameters: -> - {% icon param-file %} *"Assembly to clean"*: `genome_masked.fasta` (Input dataset) -> -> 2. {% tool [Sort assembly](toolshed.g2.bx.psu.edu/repos/iuc/funannotate_sort/funannotate_sort/1.8.9+galaxy2) %} with the following parameters: -> - {% icon param-file %} *"Assembly to sort"*: `output` (output of **Funannotate assembly clean** {% icon tool %}) -> -{: .hands_on} - -After this step, the genome is clean, sorted, and ready for the structural annotation. - -> -> -> How many sequences are removed by this cleaning step ? -> -> > -> > -> > The repeat masked genome contains 1461 sequences, while the cleand one only contains 1425, so 36 were removed. -> > -> {: .solution} -> -{: .question} - # Preparing RNASeq data When you sequence a new genome, you usually sequence a few libraries of RNASeq data, from different tissues and in different conditions, because this data will help you in annotating the genome. Here, we are using data from one RNASeq dataset that is available on [Sequence Read Archive (SRA)](https://www.ncbi.nlm.nih.gov/sra): [SRR8534859](https://www.ncbi.nlm.nih.gov/sra/?term=SRR8534859). @@ -157,7 +123,7 @@ To make use of this RNASeq data, we need to map it on the genome. We will use ** > - {% icon param-file %} *"RNA-Seq FASTQ/FASTA file, forward reads"*: `rnaseq_R1.fq.gz` (Input dataset) > - {% icon param-file %} *"RNA-Seq FASTQ/FASTA file, reverse reads"*: `rnaseq_R2.fq.gz` (Input dataset) > - *"Custom or built-in reference genome"*: `Use reference genome from history and create temporary index` -> - {% icon param-file %} *"Select a reference genome"*: `genome` (output of **Sort assembly** {% icon tool %}) +> - {% icon param-file %} *"Select a reference genome"*: `genome_masked.fasta` (Input dataset) > - *"Length of the SA pre-indexing string"*: `11` > {: .hands_on} @@ -196,8 +162,8 @@ Funannotate is also able to use GeneMark to predict new genes, but to due to lic > > -> 1. {% tool [Funannotate predict annotation](toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.9+galaxy2) %} with the following parameters: -> - {% icon param-file %} *"Assembly to annotate"*: `genome` (output of **Sort assembly** {% icon tool %}) +> 1. {% tool [Funannotate predict annotation](toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy1) %} with the following parameters: +> - {% icon param-file %} *"Assembly to annotate"*: `genome_masked.fasta` (Input dataset) > - *"Funannotate database"*: select the latest version available > - In *"Organism"*: > - *"Name of the species to annotate"*: `Mucor mucedo` @@ -274,7 +240,7 @@ Now we have a structural annotation, and the results of both **EggNOG Mapper** a > > -> 1. {% tool [Funannotate functional](toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.9+galaxy2) %} with the following parameters: +> 1. {% tool [Funannotate functional](toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy1) %} with the following parameters: > - *"Input format"*: `GenBank (from 'Funannotate predict annotation' tool)` > - {% icon param-file %} *"Genome annotation in genbank format"*: `annotation (genbank)` (output of **Funannotate predict annotation** {% icon tool %}) > - *"Funannotate database"*: select the latest version available @@ -303,7 +269,7 @@ We now have a complete annotation, including functional annotation, but it's tim > > -> 1. {% tool [Busco](toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2) %} with the following parameters: +> 1. {% tool [Busco](toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0) %} with the following parameters: > - {% icon param-file %} *"Sequences to analyse"*: `protein sequences` (output of **Funannotate functional** {% icon tool %}) > - *"Mode"*: `annotated gene sets (protein)` > - *"Auto-detect or select lineage?"*: `Select lineage` @@ -336,7 +302,7 @@ With Galaxy, you can visualize the annotation you have generated using JBrowse g > > 1. {% tool [JBrowse](toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1) %} with the following parameters: > - *"Reference genome to display"*: `Use a genome from history` -> - {% icon param-file %} *"Select the reference genome"*: `genome` (output of **Sort assembly** {% icon tool %}) +> - {% icon param-file %} *"Select the reference genome"*: `genome_masked.fasta` (Input dataset) > - In *"Track Group"*: > - {% icon param-repeat %} *"Insert Track Group"* > - *"Track Category"*: `Annotation` @@ -416,7 +382,7 @@ The output is a web page where you can see how many loci or genes are identical > > -> 1. {% tool [Funannotate compare](toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.9+galaxy2) %} with the following parameters: +> 1. {% tool [Funannotate compare](toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy1) %} with the following parameters: > - {% icon param-files %} *"Genome annotations in genbank format"*: `alternate_annotation.gbk` (Input dataset) and `gbk` (output of **Funannotate functional** {% icon tool %}) > - *"Funannotate database"*: select the latest version available > diff --git a/topics/genome-annotation/tutorials/funannotate/workflows/funannotate-tests.yml b/topics/genome-annotation/tutorials/funannotate/workflows/funannotate-tests.yml index 89ac44cae0e877..581821fd479a4c 100644 --- a/topics/genome-annotation/tutorials/funannotate/workflows/funannotate-tests.yml +++ b/topics/genome-annotation/tutorials/funannotate/workflows/funannotate-tests.yml @@ -3,15 +3,15 @@ Alternate annotation gbk: class: File filetype: genbank - location: https://zenodo.org/api/files/8c2cc766-2b68-45bd-a2d3-391acf9bdb1b/alternate_annotation.gbk + location: https://zenodo.org/api/files/47406781-e8af-42e7-855d-d29e4a098f6f/alternate_annotation.gbk Alternate annotation gff3: class: File filetype: gff3 - location: https://zenodo.org/api/files/8c2cc766-2b68-45bd-a2d3-391acf9bdb1b/alternate_annotation.gff3 + location: https://zenodo.org/api/files/47406781-e8af-42e7-855d-d29e4a098f6f/alternate_annotation.gff3 Genome assembly: class: File filetype: fasta - location: https://zenodo.org/api/files/8c2cc766-2b68-45bd-a2d3-391acf9bdb1b/genome_masked.fasta + location: https://zenodo.org/api/files/47406781-e8af-42e7-855d-d29e4a098f6f/genome_masked.fasta NCBI submission template: class: File filetype: txt @@ -19,15 +19,15 @@ Protein evidence sequences: class: File filetype: fasta - location: https://zenodo.org/api/files/8c2cc766-2b68-45bd-a2d3-391acf9bdb1b/SwissProt_subset.fasta + location: https://zenodo.org/api/files/47406781-e8af-42e7-855d-d29e4a098f6f/SwissProt_subset.fasta RNASeq reads forward: class: File filetype: fastqsanger.gz - location: https://zenodo.org/api/files/8c2cc766-2b68-45bd-a2d3-391acf9bdb1b/rnaseq_R1.fq.gz + location: https://zenodo.org/api/files/47406781-e8af-42e7-855d-d29e4a098f6f/rnaseq_R1.fq.gz RNASeq reads reverse: class: File filetype: fastqsanger.gz - location: https://zenodo.org/api/files/8c2cc766-2b68-45bd-a2d3-391acf9bdb1b/rnaseq_R2.fq.gz + location: https://zenodo.org/api/files/47406781-e8af-42e7-855d-d29e4a098f6f/rnaseq_R2.fq.gz outputs: 'Busco summary': file: 'test-data/busco_sum.txt' diff --git a/topics/genome-annotation/tutorials/funannotate/workflows/main_workflow.ga b/topics/genome-annotation/tutorials/funannotate/workflows/funannotate.ga similarity index 69% rename from topics/genome-annotation/tutorials/funannotate/workflows/main_workflow.ga rename to topics/genome-annotation/tutorials/funannotate/workflows/funannotate.ga index 7bd10b1f22824d..e3febc6b62b8e9 100644 --- a/topics/genome-annotation/tutorials/funannotate/workflows/main_workflow.ga +++ b/topics/genome-annotation/tutorials/funannotate/workflows/funannotate.ga @@ -13,163 +13,133 @@ "name": "Funannotate", "steps": { "0": { - "annotation": "Some RNASeq data, reverse reads, in fastq format", + "annotation": "The genome sequence that you wish to annotate, in fasta format. It needs to be soft masked beforehand.", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { - "description": "Some RNASeq data, reverse reads, in fastq format", - "name": "RNASeq reads reverse" + "description": "The genome sequence that you wish to annotate, in fasta format. It needs to be soft masked beforehand.", + "name": "Genome assembly" } ], - "label": "RNASeq reads reverse", + "label": "Genome assembly", "name": "Input dataset", "outputs": [], "position": { - "bottom": 27.094446818033852, - "height": 61.65000915527344, - "left": -876.4444173177084, - "right": -726.4444173177084, - "top": -34.555562337239586, - "width": 150, - "x": -876.4444173177084, - "y": -34.555562337239586 + "left": 0, + "top": 7.75 }, "tool_id": null, - "tool_state": "{\"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "160023e3-250f-424d-abe5-f7e3978768f0", + "uuid": "cca15c08-8dd9-424a-8260-4c02a94c2612", "workflow_outputs": [] }, "1": { - "annotation": "Some protein sequences to align on the genome to help annotation", + "annotation": "Some RNASeq data, forward reads, in fastq format", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "Some protein sequences to align on the genome to help annotation", - "name": "Protein evidence sequences" + "description": "Some RNASeq data, forward reads, in fastq format", + "name": "RNASeq reads forward" } ], - "label": "Protein evidence sequences", + "label": "RNASeq reads forward", "name": "Input dataset", "outputs": [], "position": { - "bottom": 157.85000101725262, - "height": 61.65000915527344, - "left": -875.3333333333334, - "right": -725.3333333333334, - "top": 96.19999186197917, - "width": 150, - "x": -875.3333333333334, - "y": 96.19999186197917 + "left": 3.45001220703125, + "top": 164.33334350585938 }, "tool_id": null, - "tool_state": "{\"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "abb56aaf-5988-4fb8-a68f-0edaee00f445", + "uuid": "6681e7b9-68f6-46e4-811f-60473d23fe0f", "workflow_outputs": [] }, "2": { - "annotation": "Some RNASeq data, forward reads, in fastq format", + "annotation": "Some RNASeq data, reverse reads, in fastq format", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { - "description": "Some RNASeq data, forward reads, in fastq format", - "name": "RNASeq reads forward" + "description": "Some RNASeq data, reverse reads, in fastq format", + "name": "RNASeq reads reverse" } ], - "label": "RNASeq reads forward", + "label": "RNASeq reads reverse", "name": "Input dataset", "outputs": [], "position": { - "bottom": -119.23888651529947, - "height": 61.65000915527344, - "left": -879, - "right": -729, - "top": -180.8888956705729, - "width": 150, - "x": -879, - "y": -180.8888956705729 + "left": 6, + "top": 310.6666564941406 }, "tool_id": null, - "tool_state": "{\"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "6681e7b9-68f6-46e4-811f-60473d23fe0f", + "uuid": "160023e3-250f-424d-abe5-f7e3978768f0", "workflow_outputs": [] }, "3": { - "annotation": "A submission template retrieved from NCBI (generate it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/)", + "annotation": "Some protein sequences to align on the genome to help annotation", "content_id": null, "errors": null, "id": 3, "input_connections": {}, "inputs": [ { - "description": "A submission template retrieved from NCBI (generate it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/)", - "name": "NCBI submission template" + "description": "Some protein sequences to align on the genome to help annotation", + "name": "Protein evidence sequences" } ], - "label": "NCBI submission template", + "label": "Protein evidence sequences", "name": "Input dataset", "outputs": [], "position": { - "bottom": 296.9166717529297, - "height": 61.65000915527344, - "left": -880, - "right": -730, - "top": 235.26666259765625, - "width": 150, - "x": -880, - "y": 235.26666259765625 + "left": 7.116668701171875, + "top": 441.4166564941406 }, "tool_id": null, - "tool_state": "{\"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "537f8bb4-4986-4d8d-a49b-1842dfaa739a", + "uuid": "abb56aaf-5988-4fb8-a68f-0edaee00f445", "workflow_outputs": [] }, "4": { - "annotation": "The genome sequence that you wish to annotate, in fasta format. It needs to be soft masked beforehand.", + "annotation": "A submission template retrieved from NCBI (generate it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/)", "content_id": null, "errors": null, "id": 4, "input_connections": {}, "inputs": [ { - "description": "The genome sequence that you wish to annotate, in fasta format. It needs to be soft masked beforehand.", - "name": "Genome assembly" + "description": "A submission template retrieved from NCBI (generate it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/)", + "name": "NCBI submission template" } ], - "label": "Genome assembly", + "label": "NCBI submission template", "name": "Input dataset", "outputs": [], "position": { - "bottom": -275.81666564941406, - "height": 61.65000915527344, - "left": -882.4444173177084, - "right": -732.4444173177084, - "top": -337.4666748046875, - "width": 150, - "x": -882.4444173177084, - "y": -337.4666748046875 + "left": 2.45001220703125, + "top": 580.4833068847656 }, "tool_id": null, - "tool_state": "{\"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "cca15c08-8dd9-424a-8260-4c02a94c2612", + "uuid": "537f8bb4-4986-4d8d-a49b-1842dfaa739a", "workflow_outputs": [] }, "5": { @@ -188,17 +158,11 @@ "name": "Input dataset", "outputs": [], "position": { - "bottom": 444.16111755371094, - "height": 61.65000915527344, - "left": -882.4444173177084, - "right": -732.4444173177084, - "top": 382.5111083984375, - "width": 150, - "x": -882.4444173177084, - "y": 382.5111083984375 + "left": 0, + "top": 727.7333068847656 }, "tool_id": null, - "tool_state": "{\"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "51a62e82-d478-45c3-bcbc-f38f1fd85974", @@ -220,17 +184,11 @@ "name": "Input dataset", "outputs": [], "position": { - "bottom": 562.1833343505859, - "height": 61.65000915527344, - "left": -881.977783203125, - "right": -731.977783203125, - "top": 500.5333251953125, - "width": 150, - "x": -881.977783203125, - "y": 500.5333251953125 + "left": 0.4666748046875, + "top": 845.7500305175781 }, "tool_id": null, - "tool_state": "{\"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "e4367779-3fc7-4eec-8e45-86158b3950bc", @@ -238,125 +196,20 @@ }, "7": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_clean/funannotate_clean/1.8.9+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3", "errors": null, "id": 7, - "input_connections": { - "input": { - "id": 4, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "Funannotate assembly clean", - "outputs": [ - { - "name": "output", - "type": "fasta" - } - ], - "position": { - "bottom": -232.1999969482422, - "height": 115.80000305175781, - "left": -611.0888671875, - "right": -461.0888671875, - "top": -348, - "width": 150, - "x": -611.0888671875, - "y": -348 - }, - "post_job_actions": { - "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_clean/funannotate_clean/1.8.9+galaxy2", - "tool_shed_repository": { - "changeset_revision": "a230ea445788", - "name": "funannotate_clean", - "owner": "iuc", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"cov\": \"95\", \"exhaustive\": \"false\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"minlen\": \"500\", \"pident\": \"95\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.8.9+galaxy2", - "type": "tool", - "uuid": "8f457bb0-5d62-4fcb-bf39-5c857c29172b", - "workflow_outputs": [] - }, - "8": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_sort/funannotate_sort/1.8.9+galaxy2", - "errors": null, - "id": 8, - "input_connections": { - "input": { - "id": 7, - "output_name": "output" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool Sort assembly", - "name": "input" - } - ], - "label": null, - "name": "Sort assembly", - "outputs": [ - { - "name": "output", - "type": "fasta" - } - ], - "position": { - "bottom": -264.1333363850911, - "height": 85.19999694824219, - "left": -355.5111083984375, - "right": -205.5111083984375, - "top": -349.3333333333333, - "width": 150, - "x": -355.5111083984375, - "y": -349.3333333333333 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_sort/funannotate_sort/1.8.9+galaxy2", - "tool_shed_repository": { - "changeset_revision": "b3cf4684e9c7", - "name": "funannotate_sort", - "owner": "iuc", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"base\": \"scaffold\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"minlen\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.8.9+galaxy2", - "type": "tool", - "uuid": "18eb051e-6b19-4d92-927d-629f2a0556ee", - "workflow_outputs": [ - { - "label": "Sorted assembly", - "output_name": "output", - "uuid": "98ef8773-bbf5-4971-b779-5c5f0b385d1d" - } - ] - }, - "9": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy0", - "errors": null, - "id": 9, "input_connections": { "refGenomeSource|genomeFastaFiles": { - "id": 8, + "id": 0, "output_name": "output" }, "singlePaired|input1": { - "id": 2, + "id": 1, "output_name": "output" }, "singlePaired|input2": { - "id": 0, + "id": 2, "output_name": "output" } }, @@ -391,14 +244,8 @@ } ], "position": { - "bottom": 131.37777709960938, - "height": 237.60000610351562, - "left": -115.75555419921875, - "right": 34.24444580078125, - "top": -106.22222900390625, - "width": 150, - "x": -115.75555419921875, - "y": -106.22222900390625 + "left": 766.699951171875, + "top": 239.0 }, "post_job_actions": { "HideDatasetActionoutput_log": { @@ -412,41 +259,41 @@ "output_name": "splice_junctions" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3", "tool_shed_repository": { - "changeset_revision": "4074fc1940e2", + "changeset_revision": "3ea5a2a63fa2", "name": "rgrnastar", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"algo\": {\"params\": {\"settingsType\": \"default\", \"__current_case__\": 0}}, \"chimOutType\": \"\", \"filter\": {\"basic_filters\": [\"exclude_unmapped\"], \"output_params2\": {\"output_select2\": \"no\", \"__current_case__\": 1}}, \"oformat\": {\"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\", \"ch\"], \"HI_offset\": \"1\", \"outSAMprimaryFlag\": \"OneBestScore\", \"outSAMmapqUnique\": \"60\"}, \"perf\": {\"outBAMsortingBinsN\": \"50\", \"winAnchorMultimapNmax\": \"50\"}, \"quantmode_output\": {\"quantMode\": \"-\", \"__current_case__\": 0}, \"refGenomeSource\": {\"geneSource\": \"history\", \"__current_case__\": 1, \"genomeFastaFiles\": {\"__class__\": \"RuntimeValue\"}, \"genomeSAindexNbases\": \"11\", \"GTFconditional\": {\"GTFselect\": \"without-gtf\", \"__current_case__\": 1}}, \"singlePaired\": {\"sPaired\": \"paired\", \"__current_case__\": 1, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"input2\": {\"__class__\": \"RuntimeValue\"}}, \"twopass\": {\"twopassMode\": \"None\", \"__current_case__\": 0, \"twopass_read_subset\": \"\", \"sj_precalculated\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.7.8a+galaxy0", + "tool_state": "{\"algo\": {\"params\": {\"settingsType\": \"default\", \"__current_case__\": 0}}, \"chimOutType\": \"\", \"filter\": {\"basic_filters\": [\"exclude_unmapped\"], \"output_params2\": {\"output_select2\": \"no\", \"__current_case__\": 1}}, \"oformat\": {\"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\", \"ch\"], \"HI_offset\": \"1\", \"outSAMprimaryFlag\": \"OneBestScore\", \"outSAMmapqUnique\": \"60\"}, \"outWig\": {\"outWigType\": \"None\", \"__current_case__\": 0, \"outWigStrand\": \"false\"}, \"perf\": {\"outBAMsortingBinsN\": \"50\", \"winAnchorMultimapNmax\": \"50\"}, \"refGenomeSource\": {\"geneSource\": \"history\", \"__current_case__\": 1, \"genomeFastaFiles\": {\"__class__\": \"RuntimeValue\"}, \"genomeSAindexNbases\": \"11\", \"GTFconditional\": {\"GTFselect\": \"without-gtf\", \"__current_case__\": 1, \"quantmode_output\": {\"quantMode\": \"-\", \"__current_case__\": 0}}}, \"singlePaired\": {\"sPaired\": \"paired\", \"__current_case__\": 1, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"input2\": {\"__class__\": \"RuntimeValue\"}}, \"twopass\": {\"twopassMode\": \"None\", \"__current_case__\": 0, \"twopass_read_subset\": \"\", \"sj_precalculated\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.7.10b+galaxy3", "type": "tool", "uuid": "269a3794-e421-4826-a5de-8a328fd194bd", "workflow_outputs": [ { "label": "Mapped RNASeq", "output_name": "mapped_reads", - "uuid": "84af1786-2381-4f59-86db-77e3abbbe922" + "uuid": "79cf59ea-3aef-4cb8-9c70-5b42e03a5da9" } ] }, - "10": { + "8": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.9+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy0", "errors": null, - "id": 10, + "id": 8, "input_connections": { "evidences|prot_evidence|protein_evidence": { - "id": 1, + "id": 3, "output_name": "output" }, "evidences|rna_bam": { - "id": 9, + "id": 7, "output_name": "mapped_reads" }, "input": { - "id": 8, + "id": 0, "output_name": "output" } }, @@ -459,6 +306,10 @@ "description": "runtime parameter for tool Funannotate predict annotation", "name": "evidences" }, + { + "description": "runtime parameter for tool Funannotate predict annotation", + "name": "evidences" + }, { "description": "runtime parameter for tool Funannotate predict annotation", "name": "genemark" @@ -467,6 +318,10 @@ "description": "runtime parameter for tool Funannotate predict annotation", "name": "genemark" }, + { + "description": "runtime parameter for tool Funannotate predict annotation", + "name": "input" + }, { "description": "runtime parameter for tool Funannotate predict annotation", "name": "other_predictors" @@ -533,14 +388,8 @@ } ], "position": { - "bottom": 820.4667154947917, - "height": 1099.800048828125, - "left": 172.82222493489584, - "right": 322.82222493489587, - "top": -279.3333333333333, - "width": 150, - "x": 172.82222493489584, - "y": -279.3333333333333 + "left": 1055.2666015625, + "top": 65.88333129882812 }, "post_job_actions": { "HideDatasetActionannot_gbk": { @@ -589,40 +438,40 @@ "output_name": "tbl2asn_validation" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.9+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy0", "tool_shed_repository": { - "changeset_revision": "2bba2ff070d9", + "changeset_revision": "51b6ee65ef7f", "name": "funannotate_predict", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"augustus\": {\"augustus_species\": \"none\", \"min_training_models\": \"200\", \"optimize_augustus\": \"false\"}, \"busco\": {\"busco_db\": \"mucorales_odb10\", \"busco_seed_species\": \"rhizopus_oryzae\"}, \"database\": {\"__class__\": \"RuntimeValue\"}, \"evidences\": {\"rna_bam\": {\"__class__\": \"ConnectedValue\"}, \"transcript_evidence\": {\"__class__\": \"RuntimeValue\"}, \"prot_evidence\": {\"prot_evidence_source\": \"custom\", \"__current_case__\": 1, \"protein_evidence\": {\"__class__\": \"ConnectedValue\"}}, \"p2g_pident\": \"80\", \"p2g_prefilter\": \"diamond\"}, \"evm\": {\"repeats2evm\": \"false\", \"evm_partitioning\": {\"evm_partition\": \"yes\", \"__current_case__\": 0, \"evm_partition_interval\": \"1500\"}, \"weights\": \"\"}, \"filtering\": {\"min_intronlen\": \"10\", \"max_intronlen\": \"3000\", \"min_protlen\": \"50\", \"keep_no_stops\": \"false\", \"repeat_filter\": \"overlap blast\"}, \"force\": \"true\", \"genemark\": {\"genemark_license\": {\"__class__\": \"RuntimeValue\"}, \"genemark_mode\": \"ES\", \"genemark_mod\": {\"__class__\": \"RuntimeValue\"}, \"soft_mask\": \"2000\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"organism\": {\"species\": \"Mucor mucedo\", \"isolate\": \"\", \"strain\": \"muc1\", \"organism\": \"false\", \"ploidy\": \"1\", \"SeqCenter\": \"CFMR\", \"SeqAccession\": \"12345\", \"name\": \"FUN_\", \"numbering\": \"1\"}, \"other_predictors\": {\"stringtie\": {\"__class__\": \"RuntimeValue\"}, \"maker_gff\": {\"__class__\": \"RuntimeValue\"}, \"pasa_gff\": {\"__class__\": \"RuntimeValue\"}, \"pasa_gff_weight\": \"1\", \"other_gff\": {\"__class__\": \"RuntimeValue\"}, \"other_gff_weight\": \"1\"}, \"outputs\": [\"gbk\", \"tbl\", \"gff3\", \"proteins_fa\", \"mrna_transcripts_fa\", \"cds_transcripts_fa\", \"tbl2asn_report\", \"tbl2asn_error\", \"tbl2asn_validation\", \"stats\"], \"parameters\": {\"__class__\": \"RuntimeValue\"}, \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.8.9+galaxy2", + "tool_state": "{\"augustus\": {\"augustus_species\": \"none\", \"min_training_models\": \"200\", \"optimize_augustus\": \"false\"}, \"busco\": {\"busco_db\": \"mucorales_odb10\", \"busco_seed_species\": \"rhizopus_oryzae\"}, \"database\": {\"__class__\": \"RuntimeValue\"}, \"evidences\": {\"rna_bam\": {\"__class__\": \"RuntimeValue\"}, \"transcript_evidence\": {\"__class__\": \"RuntimeValue\"}, \"prot_evidence\": {\"prot_evidence_source\": \"custom\", \"__current_case__\": 1, \"protein_evidence\": {\"__class__\": \"RuntimeValue\"}}, \"p2g_pident\": \"80\", \"p2g_prefilter\": \"diamond\"}, \"evm\": {\"repeats2evm\": \"false\", \"evm_partitioning\": {\"evm_partition\": \"yes\", \"__current_case__\": 0, \"evm_partition_interval\": \"1500\"}, \"weights\": \"\"}, \"filtering\": {\"min_intronlen\": \"10\", \"max_intronlen\": \"3000\", \"min_protlen\": \"50\", \"keep_no_stops\": \"false\", \"repeat_filter\": \"overlap blast\"}, \"force\": \"true\", \"genemark\": {\"genemark_license\": {\"__class__\": \"RuntimeValue\"}, \"genemark_mode\": \"ES\", \"genemark_mod\": {\"__class__\": \"RuntimeValue\"}, \"soft_mask\": \"2000\"}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"organism\": {\"species\": \"Mucor mucedo\", \"isolate\": \"\", \"strain\": \"muc1\", \"organism\": \"false\", \"ploidy\": \"1\", \"SeqCenter\": \"CFMR\", \"SeqAccession\": \"12345\", \"name\": \"FUN_\", \"numbering\": \"1\"}, \"other_predictors\": {\"stringtie\": {\"__class__\": \"RuntimeValue\"}, \"maker_gff\": {\"__class__\": \"RuntimeValue\"}, \"pasa_gff\": {\"__class__\": \"RuntimeValue\"}, \"pasa_gff_weight\": \"1\", \"other_gff\": {\"__class__\": \"RuntimeValue\"}, \"other_gff_weight\": \"1\"}, \"outputs\": [\"gbk\", \"tbl\", \"gff3\", \"proteins_fa\", \"mrna_transcripts_fa\", \"cds_transcripts_fa\", \"tbl2asn_report\", \"tbl2asn_error\", \"tbl2asn_validation\", \"stats\"], \"parameters\": {\"__class__\": \"RuntimeValue\"}, \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.8.15+galaxy0", "type": "tool", "uuid": "aefc0275-b611-4ede-9650-2e16553a7352", "workflow_outputs": [ { "label": null, "output_name": "fasta_proteins", - "uuid": "26eb2776-1e2f-4f61-9c47-f6281ed0c94f" + "uuid": "aa7fb986-b7db-4353-a83b-3f1591911388" } ] }, - "11": { + "9": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.6+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3", "errors": null, - "id": 11, + "id": 9, "input_connections": { - "input": { - "id": 10, + "ortho_method|input": { + "id": 8, "output_name": "fasta_proteins" } }, "inputs": [ { "description": "runtime parameter for tool eggNOG Mapper", - "name": "input" + "name": "ortho_method" } ], "label": null, @@ -638,14 +487,8 @@ } ], "position": { - "bottom": 238.0111083984375, - "height": 184.5, - "left": 524.5111083984375, - "right": 674.5111083984375, - "top": 53.5111083984375, - "width": 150, - "x": 524.5111083984375, - "y": 53.5111083984375 + "left": 1444.9666748046875, + "top": 418.7333068847656 }, "post_job_actions": { "HideDatasetActionseed_orthologs": { @@ -654,33 +497,33 @@ "output_name": "seed_orthologs" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.6+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3", "tool_shed_repository": { - "changeset_revision": "96cac424c870", + "changeset_revision": "9d1fbff733cf", "name": "eggnog_mapper", "owner": "galaxyp", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"annotation_options\": {\"tax_scope\": null, \"target_orthologs\": \"all\", \"go_evidence\": \"non-electronic\"}, \"eggnog_data\": \"5.0.2\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"input_trans\": {\"itype\": \"proteins\", \"__current_case__\": 0}, \"output_options\": {\"no_file_comments\": \"false\", \"no_annot\": \"false\", \"report_orthologs\": \"false\"}, \"seed_ortho_options\": {\"ortho_method\": {\"m\": \"diamond\", \"__current_case__\": 0, \"matrix_gapcosts\": {\"matrix\": \"BLOSUM62\", \"__current_case__\": 2, \"gap_costs\": \"--gapopen 11 --gapextend 1\"}, \"sensmode\": \"sensitive\", \"dmnd_iterate\": \"false\", \"dmnd_ignore_warnings\": \"false\"}, \"query_cover\": null, \"subject_cover\": null, \"pident\": null}, \"seed_ortholog_options\": {\"seed_ortholog_evalue\": \"0.001\", \"seed_ortholog_score\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.1.6+galaxy1", + "tool_state": "{\"annotation_options\": {\"no_annot\": \"\", \"__current_case__\": 0, \"seed_ortholog_evalue\": \"0.001\", \"seed_ortholog_score\": null, \"tax_scope\": null, \"target_orthologs\": \"all\", \"go_evidence\": \"non-electronic\"}, \"eggnog_data\": \"5.0.2\", \"ortho_method\": {\"m\": \"diamond\", \"__current_case__\": 0, \"input\": {\"__class__\": \"RuntimeValue\"}, \"input_trans\": {\"itype\": \"proteins\", \"__current_case__\": 0}, \"matrix_gapcosts\": {\"matrix\": \"BLOSUM62\", \"__current_case__\": 2, \"gap_costs\": \"--gapopen 11 --gapextend 1\"}, \"sensmode\": \"sensitive\", \"dmnd_iterate\": \"false\", \"dmnd_ignore_warnings\": \"false\", \"query_cover\": null, \"subject_cover\": null, \"pident\": null, \"evalue\": null, \"score\": \"0.001\"}, \"output_options\": {\"no_file_comments\": \"false\", \"report_orthologs\": \"false\", \"md5\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.1.8+galaxy3", "type": "tool", "uuid": "0d9f93f0-88b3-406b-b8f9-ecb2d74c61e9", "workflow_outputs": [ { "label": null, "output_name": "annotations", - "uuid": "a17e0d93-449b-4b89-b3fc-a55fa9a2d159" + "uuid": "521fe026-4958-4965-9414-e7074aea7860" } ] }, - "12": { + "10": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.54-87.0+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3", "errors": null, - "id": 12, + "id": 10, "input_connections": { "input": { - "id": 10, + "id": 8, "output_name": "fasta_proteins" } }, @@ -703,14 +546,8 @@ } ], "position": { - "bottom": 595.9444529215496, - "height": 123.30000305175781, - "left": 593.3999837239584, - "right": 743.3999837239584, - "top": 472.6444498697917, - "width": 150, - "x": 593.3999837239584, - "y": 472.6444498697917 + "left": 1475.8499755859375, + "top": 817.8666687011719 }, "post_job_actions": { "HideDatasetActionoutfile_xml": { @@ -719,45 +556,45 @@ "output_name": "outfile_xml" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.54-87.0+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3", "tool_shed_repository": { - "changeset_revision": "c762a1cd357e", + "changeset_revision": "74810db257cc", "name": "interproscan", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"applications\": [\"TIGRFAM\", \"SFLD\", \"SUPERFAMILY\", \"PANTHER\", \"Gene3D\", \"Hamap\", \"PrositeProfiles\", \"Coils\", \"SMART\", \"CDD\", \"PRINTS\", \"PIRSR\", \"PrositePatterns\", \"Pfam\", \"MobiDBLite\", \"PIRSF\"], \"database\": \"5.54-87.0\", \"goterms\": \"true\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"iprlookup\": \"false\", \"licensed\": {\"use\": \"true\", \"__current_case__\": 1, \"applications_licensed\": [\"Phobius\", \"SignalP_EUK\", \"TMHMM\"]}, \"oformat\": [\"TSV\", \"XML\"], \"pathways\": \"true\", \"seqtype\": \"p\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "5.54-87.0+galaxy2", + "tool_state": "{\"applications\": [\"TIGRFAM\", \"SFLD\", \"SUPERFAMILY\", \"PANTHER\", \"Gene3D\", \"Hamap\", \"PrositeProfiles\", \"Coils\", \"SMART\", \"CDD\", \"PRINTS\", \"PIRSR\", \"PrositePatterns\", \"Pfam\", \"MobiDBLite\", \"PIRSF\"], \"database\": \"5.59-91.0\", \"goterms\": \"true\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"iprlookup\": \"false\", \"licensed\": {\"use\": \"true\", \"__current_case__\": 1, \"applications_licensed\": [\"Phobius\", \"SignalP_EUK\", \"TMHMM\"]}, \"oformat\": [\"TSV\", \"XML\"], \"pathways\": \"true\", \"seqtype\": \"p\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "5.59-91.0+galaxy3", "type": "tool", "uuid": "cb7a1910-3c31-47d9-835b-f1bd16a1c3ff", "workflow_outputs": [ { "label": null, "output_name": "outfile_tsv", - "uuid": "58042cad-e025-4565-8a1a-aad215a0b17f" + "uuid": "65e267a7-d3c6-410d-9b44-f655d70d7d9a" } ] }, - "13": { + "11": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.9+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy0", "errors": null, - "id": 13, + "id": 11, "input_connections": { "eggnog": { - "id": 11, + "id": 9, "output_name": "annotations" }, "input|genbank": { - "id": 10, + "id": 8, "output_name": "annot_gbk" }, "iprscan": { - "id": 12, + "id": 10, "output_name": "outfile_xml" }, "sbt": { - "id": 3, + "id": 4, "output_name": "output" } }, @@ -872,14 +709,8 @@ } ], "position": { - "bottom": 932.0777384440104, - "height": 1175.699951171875, - "left": 994.6666666666666, - "right": 1144.6666666666665, - "top": -243.6222127278646, - "width": 150, - "x": 994.6666666666666, - "y": -243.6222127278646 + "left": 1877.11669921875, + "top": 101.59999084472656 }, "post_job_actions": { "HideDatasetActionagp": { @@ -928,71 +759,71 @@ "output_name": "tbl" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.9+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy0", "tool_shed_repository": { - "changeset_revision": "14f588312c56", + "changeset_revision": "9feee7fc49a1", "name": "funannotate_annotate", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"annotations\": {\"__class__\": \"RuntimeValue\"}, \"antismash\": {\"__class__\": \"RuntimeValue\"}, \"busco_db\": \"mucorales_odb10\", \"database\": {\"__class__\": \"RuntimeValue\"}, \"eggnog\": {\"__class__\": \"RuntimeValue\"}, \"fix\": {\"__class__\": \"RuntimeValue\"}, \"input\": {\"input_type\": \"gbk\", \"__current_case__\": 0, \"genbank\": {\"__class__\": \"RuntimeValue\"}}, \"iprscan\": {\"__class__\": \"RuntimeValue\"}, \"isolate\": \"\", \"outputs\": [\"gbk\", \"annotations\", \"contigs_fsa\", \"agp\", \"tbl\", \"sqn\", \"scaffolds_fa\", \"proteins_fa\", \"mrna_transcripts_fa\", \"cds_transcripts_fa\", \"gff3\", \"discrepency\", \"stats\", \"must_fix\", \"need_curating\", \"new_names_passed\"], \"phobius\": {\"__class__\": \"RuntimeValue\"}, \"remove\": {\"__class__\": \"RuntimeValue\"}, \"rename\": \"\", \"sbt\": {\"__class__\": \"RuntimeValue\"}, \"strain\": \"muc1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.8.9+galaxy2", + "tool_version": "1.8.15+galaxy0", "type": "tool", "uuid": "e07de1e0-8f91-4477-b951-7d97dba2e397", "workflow_outputs": [ + { + "label": "Final annotation (genbank)", + "output_name": "gbk", + "uuid": "d0694cd1-6d81-4d72-83b9-94cb57dc1502" + }, { "label": "Final annotation (CDS sequences)", "output_name": "fa_transcripts_cds", - "uuid": "d076f328-8726-4801-b87d-d4bb8f55203b" + "uuid": "9a1e7b70-1090-41ed-8637-65b7372a9f6c" }, { "label": "Final annotation (mRNA sequences)", "output_name": "fa_transcripts_mrna", - "uuid": "f5efd944-ee51-43cd-9020-ce5ffef80d33" + "uuid": "99fffa40-2196-491d-9a66-559ebf2d9561" + }, + { + "label": "Final annotation (protein sequences)", + "output_name": "fa_proteins", + "uuid": "17b03b77-0485-4176-b2b3-03bfa2d3bcb0" }, { "label": null, "output_name": "tbl2asn_report", - "uuid": "361d2e82-412d-42b6-b6cf-55adda0d28d9" + "uuid": "d3d4daec-75fe-4071-af37-c2907e46f5c1" }, { "label": null, "output_name": "stats", - "uuid": "1c444b05-b04a-4bcb-bdcf-0daf6e1dc0b1" + "uuid": "4a682ab6-8a6f-4a0f-bb0e-ba796f587ddc" }, { "label": "Final annotation (GFF3)", "output_name": "gff3", - "uuid": "4682d6dc-eec6-474f-a891-a9bdf050ff0d" - }, - { - "label": "Final annotation (genbank)", - "output_name": "gbk", - "uuid": "278a87bb-4968-4872-b45f-2d15bc144e0c" - }, - { - "label": "Final annotation (protein sequences)", - "output_name": "fa_proteins", - "uuid": "d0501071-ca3a-413b-9810-825349c11fd5" + "uuid": "4a0602fc-e6d2-43fc-9957-344707c22c05" } ] }, - "14": { + "12": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", "errors": null, - "id": 14, + "id": 12, "input_connections": { "reference_genome|genome": { - "id": 8, + "id": 0, "output_name": "output" }, "track_groups_0|data_tracks_0|data_format|annotation": { - "id": 13, + "id": 11, "output_name": "gff3" }, "track_groups_1|data_tracks_0|data_format|annotation": { - "id": 9, + "id": 7, "output_name": "mapped_reads" } }, @@ -1011,14 +842,8 @@ } ], "position": { - "bottom": -168.52223714192706, - "height": 176.70001220703125, - "left": 1270.1555989583333, - "right": 1420.1555989583333, - "top": -345.2222493489583, - "width": 150, - "x": 1270.1555989583333, - "y": -345.2222493489583 + "left": 2152.60009765625, + "top": 0.0 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1", @@ -1036,15 +861,15 @@ { "label": "JBrowse", "output_name": "output", - "uuid": "7b3256fe-9d97-4311-a7c6-ef3521695505" + "uuid": "ac4d8805-f123-44d2-b30f-8ac906cc471f" } ] }, - "15": { + "13": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.9+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy0", "errors": null, - "id": 15, + "id": 13, "input_connections": { "input": [ { @@ -1052,7 +877,7 @@ "output_name": "output" }, { - "id": 13, + "id": 11, "output_name": "gbk" } ] @@ -1062,10 +887,6 @@ "description": "runtime parameter for tool Funannotate compare", "name": "database" }, - { - "description": "runtime parameter for tool Funannotate compare", - "name": "input" - }, { "description": "runtime parameter for tool Funannotate compare", "name": "proteinortho" @@ -1080,60 +901,45 @@ } ], "position": { - "bottom": 197.11111450195312, - "height": 138.60000610351562, - "left": 1435.5555013020833, - "right": 1585.5555013020833, - "top": 58.5111083984375, - "width": 150, - "x": 1435.5555013020833, - "y": 58.5111083984375 + "left": 2318, + "top": 403.7333068847656 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.9+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy0", "tool_shed_repository": { - "changeset_revision": "563a19373357", + "changeset_revision": "a7ce2601500c", "name": "funannotate_compare", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"database\": {\"__class__\": \"RuntimeValue\"}, \"go_fdr\": \"0.05\", \"heatmap_stdev\": \"1.0\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"ml\": {\"ml_method\": \"iqtree\", \"__current_case__\": 0}, \"num_orthos\": \"500\", \"proteinortho\": {\"__class__\": \"RuntimeValue\"}, \"run_dnds\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.8.9+galaxy2", + "tool_state": "{\"database\": {\"__class__\": \"RuntimeValue\"}, \"go_fdr\": \"0.05\", \"heatmap_stdev\": \"1.0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"ml\": {\"ml_method\": \"iqtree\", \"__current_case__\": 0}, \"num_orthos\": \"500\", \"proteinortho\": {\"__class__\": \"RuntimeValue\"}, \"run_dnds\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.8.15+galaxy0", "type": "tool", "uuid": "750137e5-2cac-4bec-8337-03dab562a7a5", "workflow_outputs": [ { "label": "Funannotate compare report", "output_name": "output", - "uuid": "5f136c42-303f-4eea-9fd0-cce86b7fd1df" + "uuid": "e531c81f-f6b7-4c82-a712-c562873ff714" } ] }, - "16": { + "14": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0", "errors": null, - "id": 16, + "id": 14, "input_connections": { "predictiongff3": { "id": 6, "output_name": "output" }, "referencegff3": { - "id": 13, + "id": 11, "output_name": "gff3" } }, - "inputs": [ - { - "description": "runtime parameter for tool AEGeAn ParsEval", - "name": "predictiongff3" - }, - { - "description": "runtime parameter for tool AEGeAn ParsEval", - "name": "referencegff3" - } - ], + "inputs": [], "label": null, "name": "AEGeAn ParsEval", "outputs": [ @@ -1143,14 +949,8 @@ } ], "position": { - "bottom": 406.5111083984375, - "height": 108, - "left": 1436.04443359375, - "right": 1586.04443359375, - "top": 298.5111083984375, - "width": 150, - "x": 1436.04443359375, - "y": 298.5111083984375 + "left": 2318.5, + "top": 643.7333068847656 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0", @@ -1160,7 +960,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"delta\": \"0\", \"maxtrans\": \"32\", \"output_type\": \"html\", \"predictiongff3\": {\"__class__\": \"RuntimeValue\"}, \"predlabel\": \"\", \"referencegff3\": {\"__class__\": \"RuntimeValue\"}, \"refrlabel\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"delta\": \"0\", \"maxtrans\": \"32\", \"output_type\": \"html\", \"predictiongff3\": {\"__class__\": \"ConnectedValue\"}, \"predlabel\": \"\", \"referencegff3\": {\"__class__\": \"ConnectedValue\"}, \"refrlabel\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.16.0", "type": "tool", "uuid": "b5870c4b-d799-4da0-83cc-7dd5a0b049e4", @@ -1168,18 +968,18 @@ { "label": "AEGeAN report", "output_name": "output_html", - "uuid": "ec20a31b-8406-4e7e-80f4-4d971956c89d" + "uuid": "0d776b46-2c1c-4083-9f9d-a213fa62eb81" } ] }, - "17": { + "15": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0", "errors": null, - "id": 17, + "id": 15, "input_connections": { "input": { - "id": 13, + "id": 11, "output_name": "fa_proteins" } }, @@ -1206,14 +1006,8 @@ } ], "position": { - "bottom": 872.9444071451823, - "height": 146.10000610351562, - "left": 1369.822265625, - "right": 1519.822265625, - "top": 726.8444010416666, - "width": 150, - "x": 1369.822265625, - "y": 726.8444010416666 + "left": 2252.2666015625, + "top": 1072.0666809082031 }, "post_job_actions": { "HideDatasetActionbusco_table": { @@ -1222,27 +1016,27 @@ "output_name": "busco_table" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0", "tool_shed_repository": { - "changeset_revision": "46ae58b1d792", + "changeset_revision": "94170eee0ad8", "name": "busco", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\"}, \"busco_mode\": {\"mode\": \"prot\", \"__current_case__\": 2}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": \"mucorales_odb10\"}, \"outputs\": [\"short_summary\", \"image\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "5.2.2+galaxy2", + "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\"}, \"busco_mode\": {\"mode\": \"prot\", \"__current_case__\": 2}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": \"mucorales_odb10\"}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"image\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "5.4.6+galaxy0", "type": "tool", "uuid": "bec3d4d9-88e6-4ea0-beb6-219d5c727290", "workflow_outputs": [ - { - "label": "Busco image", - "output_name": "summary_image", - "uuid": "7ee4ddad-e860-4049-b8fa-5030807ff29f" - }, { "label": "Busco summary", "output_name": "busco_sum", - "uuid": "6a3fa0e4-87e0-40d9-9d77-9ab9f6b91d2c" + "uuid": "57a619f5-b331-4ca6-8e6e-72eb61860032" + }, + { + "label": "Busco image", + "output_name": "summary_image", + "uuid": "97d23764-ad4a-4d69-948c-c81afb76fbaf" } ] } @@ -1250,6 +1044,6 @@ "tags": [ "genome-annotation" ], - "uuid": "649af106-a0c6-49d8-9a31-63a68d978c0b", - "version": 53 -} + "uuid": "cb81783b-75a8-427b-9013-1a75cda50f88", + "version": 57 +} \ No newline at end of file diff --git a/topics/genome-annotation/tutorials/functional/content.md b/topics/genome-annotation/tutorials/functional/content.md index e9dc915f240edf..3f7faa445bc79d 100644 --- a/topics/genome-annotation/tutorials/functional/content.md +++ b/topics/genome-annotation/tutorials/functional/content.md @@ -12,7 +12,7 @@ > > -> 1. {% tool [eggNOG Mapper](toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy2.1.8) %} with the following parameters: +> 1. {% tool [eggNOG Mapper](toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3) %} with the following parameters: > - {% icon param-file %} *"Fasta sequences to annotate"*: {{ input_dataset }} > - *"Version of eggNOG Database"*: select the latest version available > - In *"Output Options"*: @@ -34,7 +34,7 @@ Display the file and explore which kind of identifiers were found by EggNOG Mapp > > -> 1. {% tool [InterProScan](toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.55-88.0+galaxy3) %} with the following parameters: +> 1. {% tool [InterProScan](toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3) %} with the following parameters: > - {% icon param-file %} *"Protein FASTA File"*: {{ input_dataset }} > - *"InterProScan database"*: select the latest version available > - *"Use applications with restricted license, only for non-commercial use?"*: `Yes` (set it to `No` if you run InterProScan for commercial use) diff --git a/topics/genome-annotation/tutorials/functional/workflows/functional-tests.yml b/topics/genome-annotation/tutorials/functional/workflows/functional-tests.yml index 9307f573628517..55cdb8039f4b95 100644 --- a/topics/genome-annotation/tutorials/functional/workflows/functional-tests.yml +++ b/topics/genome-annotation/tutorials/functional/workflows/functional-tests.yml @@ -3,7 +3,7 @@ Alternate annotation gbk: class: File filetype: fasta - location: https://zenodo.org/api/files/8c2cc766-2b68-45bd-a2d3-391acf9bdb1b/alternate_annotation.gbk + location: https://zenodo.org/api/files/47406781-e8af-42e7-855d-d29e4a098f6f/alternate_annotation.gbk outputs: 'EggNOG Mapper annotations': asserts: diff --git a/topics/genome-annotation/tutorials/functional/workflows/main_workflow.ga b/topics/genome-annotation/tutorials/functional/workflows/main_workflow.ga index c4811fe6e9efa4..d5572cbf160266 100644 --- a/topics/genome-annotation/tutorials/functional/workflows/main_workflow.ga +++ b/topics/genome-annotation/tutorials/functional/workflows/main_workflow.ga @@ -46,7 +46,7 @@ }, "1": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy2.1.8", + "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3", "errors": null, "id": 1, "input_connections": { @@ -97,7 +97,7 @@ "output_name": "annotations" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy2.1.8", + "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3", "tool_shed_repository": { "changeset_revision": "5a30ae278db0", "name": "eggnog_mapper", @@ -105,7 +105,7 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"annotation_options\": {\"tax_scope\": null, \"target_orthologs\": \"all\", \"go_evidence\": \"non-electronic\"}, \"eggnog_data\": \"5.0.2\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"input_trans\": {\"itype\": \"proteins\", \"__current_case__\": 0}, \"output_options\": {\"no_file_comments\": \"false\", \"no_annot\": \"false\", \"report_orthologs\": \"false\"}, \"seed_ortho_options\": {\"ortho_method\": {\"m\": \"diamond\", \"__current_case__\": 0, \"matrix_gapcosts\": {\"matrix\": \"BLOSUM62\", \"__current_case__\": 2, \"gap_costs\": \"--gapopen 11 --gapextend 1\"}, \"sensmode\": \"sensitive\", \"dmnd_iterate\": \"false\", \"dmnd_ignore_warnings\": \"false\"}, \"query_cover\": null, \"subject_cover\": null, \"pident\": null}, \"seed_ortholog_options\": {\"seed_ortholog_evalue\": \"0.001\", \"seed_ortholog_score\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.1.8+galaxy2.1.8", + "tool_version": "2.1.8+galaxy3", "type": "tool", "uuid": "0d9f93f0-88b3-406b-b8f9-ecb2d74c61e9", "workflow_outputs": [ @@ -118,7 +118,7 @@ }, "2": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.55-88.0+galaxy3", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3", "errors": null, "id": 2, "input_connections": { @@ -169,15 +169,15 @@ "output_name": "outfile_tsv" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.55-88.0+galaxy3", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3", "tool_shed_repository": { "changeset_revision": "98cafcbd2578", "name": "interproscan", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"applications\": [\"TIGRFAM\", \"SFLD\", \"SUPERFAMILY\", \"PANTHER\", \"Gene3D\", \"Hamap\", \"PrositeProfiles\", \"Coils\", \"SMART\", \"CDD\", \"PRINTS\", \"PIRSR\", \"PrositePatterns\", \"Pfam\", \"MobiDBLite\", \"PIRSF\"], \"database\": \"5.55-88.0\", \"goterms\": \"true\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"iprlookup\": \"false\", \"licensed\": {\"use\": \"true\", \"__current_case__\": 1, \"applications_licensed\": [\"Phobius\", \"SignalP_EUK\", \"TMHMM\"]}, \"oformat\": [\"TSV\", \"XML\"], \"pathways\": \"true\", \"seqtype\": \"p\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "5.55-88.0+galaxy3", + "tool_state": "{\"applications\": [\"TIGRFAM\", \"SFLD\", \"SUPERFAMILY\", \"PANTHER\", \"Gene3D\", \"Hamap\", \"PrositeProfiles\", \"Coils\", \"SMART\", \"CDD\", \"PRINTS\", \"PIRSR\", \"PrositePatterns\", \"Pfam\", \"MobiDBLite\", \"PIRSF\"], \"database\": \"5.59-91.0\", \"goterms\": \"true\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"iprlookup\": \"false\", \"licensed\": {\"use\": \"true\", \"__current_case__\": 1, \"applications_licensed\": [\"Phobius\", \"SignalP_EUK\", \"TMHMM\"]}, \"oformat\": [\"TSV\", \"XML\"], \"pathways\": \"true\", \"seqtype\": \"p\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "5.59-91.0+galaxy3", "type": "tool", "uuid": "cb7a1910-3c31-47d9-835b-f1bd16a1c3ff", "workflow_outputs": [