Release ProteoRE 2.1 : Tool panel new version

[yvandenb]

List of tools (ordered according to the tool panel) and associated tasks: ongoing

[combesf]

Here is a proposal for the tool panel of the v2.1 I added if the tool is new or updated, but this is for us (not to appear in the online version) Feel free to improve/complete ...

DATA MANIPULATION AND VISUALIZATION ID Converter (Human, Mouse, Rat) update Filter by keywords and/or numerical value Venn diagram [JVenn] update Volcano Plot create a volcano plot new HeatMap (Cluster and visualize the results)

HUMAN ANNOTATION Get expression profiles by (normal or tumor) tissue/cell type [Human Protein Atlas] Add expression data (RNAseq or Immuno-assays)[Human Protein Atlas] Add protein features [neXtProt] Get MS/MS observations in tissue/fluid [Peptide Atlas] Get unique peptide SRM-MRM method [SRM Atlas] Build tissue-specific expression dataset [Human Protein Atlas](no input required)

Human, Mouse and Rat ANNOTATION Add protein features (3 orga) [UniProt] new

GO TERMS ANALYSIS Statistical analysis of functional profiles (Human, Mouse) [goProfiles] GO terms classification and enrichment analysis (Human, Mouse, Rat)[clusterProfiler] update GO terms enrich comparison (Human, Mouse, Rat)[clusterProfiler] new Enrichment analysis for Gene Ontology (Human, Mouse, Rat)[topGO]

PATHWAY ANALYSIS Query pathway database [Reactome] Pathways identification and coverage [KEGG] Pathways visualization of (differentially expressed) genes/proteins [KEGG] update Build Protein-Protein interaction network [BioGRID, BioPlex, HuMAP]

[yvandenb]

Great Flo! with my suggestions included below + en GRAS les noms d'outils qui changent ATTENTION!: l'ordre est important et il n'y plus que 4 sections !

DATA MANIPULATION AND VISUALIZATION ID Converter (Human, Mouse, Rat) updated Filter by keywords and/or numerical value Venn diagram [JVenn] updated Draw Volcano Plot new HeatMap (clustering and visualization)

GET FEATURES/ANNOTATION Add protein features [UniProt, Human, Mouse, Rat] new Add protein features [neXtProt, Human] Get expression profiles by (normal or tumor) tissue/cell type [Human Protein Atlas] Add expression data (RNAseq or Immuno-assays)[Human Protein Atlas] Build tissue-specific expression dataset [Human Protein Atlas] Get MS/MS observations in tissue/fluid [Human Peptide Atlas] Get unique peptide SRM-MRM method [Human SRM Atlas]

FUNCTIONAL ANALYSIS Compute functional profiles (Human, Mouse) [goProfiles] Classification and enrichment analysis (Human, Mouse, Rat) [clusterProfiler] updated Biological theme comparison (Human, Mouse, Rat) [clusterProfiler] new Enrichment analysis (Human, Mouse, Rat) [topGO]

PATHWAY ANALYSIS Pathway enrichment analysis [Reactome] KEGG pathways mapping and coverage [PathView] KEGG pathways mapping and visualization [PathView] updated Build Protein interaction network [BioGRID, BioPlex, HuMAP]

[combesf]

as discussed today, I made a wiki page where to find the equivalence between sections and tools names there : https://github.com/ifb-git/ProteoRE/wiki/V2.1-tools-name-equivalence

[yvandenb]

TODO list :

• [ ] ProteoRE subSection: replace "HUMAN ANNOTATION" by "GET FEATURES/ANNOTATION

Tool name:

• [ ] rename "Get unique peptide SRM-MRM method [SRM Atlas]" as "Get unique peptide SRM-MRM method [Human SRM Atlas]
• [ ] rename "GO terms classification and enrichment analysis (Human, Mouse, Rat)[clusterProfiler]" as "Classification and enrichment analysis (Human, Mouse, Rat)[clusterProfiler]"
• [ ] rename "GO terms enrich comparison (Human, Mouse, Rat)[clusterProfiler]" as "Biological theme comparison (Human, Mouse, Rat) [clusterProfiler]"

In addition, re-organize main section as follow: ProteoRE Galaxy-P Tools Text Manipulation and then the remaining sections listed below NB!: remove/hide the "Beta tools" section

[combesf]

TODO list :

• [ ] ProteoRE subSection: replace "HUMAN ANNOTATION" by "GET FEATURES/ANNOTATION

==> to be discussed tomorrow on the phone

Tool name:

• [x] rename "Get unique peptide SRM-MRM method [SRM Atlas]" as "Get unique peptide SRM-MRM method [Human SRM Atlas]

==> done

• [x] rename "GO terms classification and enrichment analysis (Human, Mouse, Rat)[clusterProfiler]" as "Classification and enrichment analysis (Human, Mouse, Rat)[clusterProfiler]"

==> done. BUT we have a pb for this tool : there is 2 folders on the GitHub that can be for this tool : "cluster_profiler" and "GO_terms_profiles_comparison" I think the right one is "GO_terms_profiles_comparison", but to check with David. And then we have to remove the wrong folder.

• [x] rename "GO terms enrich comparison (Human, Mouse, Rat)[clusterProfiler]" as "Biological theme comparison (Human, Mouse, Rat) [clusterProfiler]"

==> cannot be done. On proteore , this tool has been installed from the main TS. But, when I want to update it to rename it, planemo tells me that it cannot update the tool caus it does not exist on the main TS. But it is there : https://toolshed.g2.bx.psu.edu/repository?repository_id=505eb7d912961a8f&changeset_revision=f53249651add

To be discussed.

In addition, re-organize main section as follow: ProteoRE Galaxy-P Tools Text Manipulation and then the remaining sections listed below NB!: remove/hide the "Beta tools" section

[yvandenb]

there is a naming confusion in the "GO terms analysis" section (that be "Functional analysis")

1. Tool currently named "Classification and enrichment analysis (Human, Mouse, Rat)[clusterProfiler] (Galaxy Version 2020.01.24)" should be named "Biological theme comparison (Human, Mouse, Rat) [clusterProfiler]" as it does not perform "Classif and enrichment analysis"
2. Tool currently "GO terms enrich comparison (Human, Mouse, Rat)[clusterProfiler] (Galaxy Version 2020.01.23)" also performs "Bioloigical theme comparison ..." but is another version and should be removed from the tool panel
3. At last, the tool that actually performs "Classif and enrichment analysis [Cluster profiler] is not there anymore ??

[combesf]

To better understand eache other : there is 4 tools in the "GO section" My view of this section:

1st is based on goProfiles -> ok 2d is based on clusterprofiler and is the 1st level tool of clusterprofiler. The tool installed is the right one with the rught name. 3d is based on clusterprofiler but to compare lists (compareCluster function). The tool is the right one but has to be renamed (not possible for the moment : why ?) 4th is based on topGO -> ok

[combesf]

ok Yves you're right : the 2d one is a wrong version

[yvandenb]

2d is based on clusterprofiler and is the 1st level tool of clusterprofiler. The tool installed is the right one with the rught name. clearly not if you look at the interface (see below) :-/ Please 1. check this very carefully, 2. fix it, 3. verify and 4. then tell us

[combesf]

there is a naming confusion in the "GO terms analysis" section (that be "Functional analysis")

1. Tool currently named "Classification and enrichment analysis (Human, Mouse, Rat)[clusterProfiler] (Galaxy Version 2020.01.24)" should be named "Biological theme comparison (Human, Mouse, Rat) [clusterProfiler]" as it does not perform "Classif and enrichment analysis"
2. Tool currently "GO terms enrich comparison (Human, Mouse, Rat)[clusterProfiler] (Galaxy Version 2020.01.23)" also performs "Bioloigical theme comparison ..." but is another version and should be removed from the tool panel

==> has been removed

3. At last, the tool that actually performs "Classif and enrichment analysis [Cluster profiler] is not there anymore ??

==> is back

[combesf]

I tried to rename the section name of the Tool Panel (Human annotation for ex.) , and the 1st section is now named "Human Annotation" and not "Data manipulation and visualization". I took the previous files but it stays like this ... hard to understand.

Anyway I think that the file to change for the section name is "config/tool_conf.xml" .. let's talk about it tomorrow morning ...

[combesf]

• [x] rename "GO terms classification and enrichment analysis (Human, Mouse, Rat)[clusterProfiler]" as "Classification and enrichment analysis (Human, Mouse, Rat)[clusterProfiler]"

==> done. BUT we have a pb for this tool : there is 2 folders on the GitHub that can be for this tool : "cluster_profiler" and "GO_terms_profiles_comparison" I think the right one is "GO_terms_profiles_comparison", but to check with David. And then we have to remove the wrong folder.

The wrong folder is the folder named "GO_terms_profiles_comparison". We'll have to delete it once all is OK on dev-migale with no confusion possible.

• [ ] rename "GO terms enrich comparison (Human, Mouse, Rat)[clusterProfiler]" as "Biological theme comparison (Human, Mouse, Rat) [clusterProfiler]"

==> cannot be done. On proteore , this tool has been installed from the main TS. But, when I want to update it to rename it, planemo tells me that it cannot update the tool caus it does not exist on the main TS. But it is there : https://toolshed.g2.bx.psu.edu/repository?repository_id=505eb7d912961a8f&changeset_revision=f53249651add

To be discussed.

I just looked at the tool id : it is the same in the xml and on the main TS and on the test TS. I really don't understand why when I run a "planemo update" it answers me : "Repository [GO_terms_enrich_comparison] does not exist in the targeted Tool Shed. Failed to update repository 'GO_terms_enrich_comparison' as it does not exist on the main Tool Shed."

It is exactly th same error message for the test TS.

I don't know what is the best : let @davidchristiany and @vloux look at this, or remove what exists on the TS to commit a new tool on the TS. Please tell me.

[davidchristiany]

I updated the tool panel of proteore-migale, tell me if it is ok for you guys.

[yvandenb]

thx David... Two things that remain to be fixed:

1. Add protein features [neXtProt, Human] is missing
2. "GO terms enrich comparison (Human, Mouse, Rat)[clusterProfiler]" to be renamed and/or replaced by "Biological theme comparison (Human, Mouse, Rat)" + gitHub to be cleaned (2 versions of this tool seems to coexist)

[davidchristiany]

I added "Add protein features [neXtProt, Human] is missing". I let @combesf rename "GO terms enrich comparison (Human, Mouse, Rat)[clusterProfiler]" and clean the git hub repository as I am not to sure what to do.

[yvandenb]

Selecting RNAseq and the version 22/01/2020, this ouptut is returned: While selecting RNAseq and the version 23/10/2018, I got the following ouput (that is the one we expected): I suspect a new confusion, in the source file used to retrieve the information As a reminder: Release date 23/10/2018: files used are : normal_tissue.tsv (for IHHC) and rna_tissue.tsv (for RNASeq); Release date 22/01/2020: files used are: normal_tissue.tsv (for IHHC) and rna_tissue_consensus.tsv (for RNASeq, HPA-GTEx-FANTOM5);

[combesf]

About the "renaming" of this tool I posted on friday on this issue:

• [ ] rename "GO terms enrich comparison (Human, Mouse, Rat)[clusterProfiler]" as "Biological theme comparison (Human, Mouse, Rat) [clusterProfiler]"

==> cannot be done. On proteore , this tool has been installed from the main TS. But, when I want to update it to rename it, planemo tells me that it cannot update the tool caus it does not exist on the main TS. But it is there : https://toolshed.g2.bx.psu.edu/repository?repository_id=505eb7d912961a8f&changeset_revision=f53249651add To be discussed.

I just looked at the tool id : it is the same in the xml and on the main TS and on the test TS. I really don't understand why when I run a "planemo update" it answers me : "Repository [GO_terms_enrich_comparison] does not exist in the targeted Tool Shed. Failed to update repository 'GO_terms_enrich_comparison' as it does not exist on the main Tool Shed."

It is exactly th same error message for the test TS.

> I don't know what is the best : let @davidchristiany and @vloux look at this, or remove what exists on the TS to commit a new tool on the TS. Please tell me.

So @davidchristiany when you write:

I let @combesf rename "GO terms enrich comparison (Human, Mouse, Rat)[clusterProfiler]" and > clean the git hub repository as I am not to sure what to do.

the answer is that I don't manage to rename this tool since last week.

[davidchristiany]

OK I can try to change the name of "GO terms enrich comparison (Human, Mouse, Rat)[clusterProfiler]", everything is up to date on github ?

For "GO_terms_profiles_comparison", I think it was the first version of your tool @combesf, the one we did together when you came at Migale ? If that's the case we can delete it. (anyway we can still find it in github history)

[combesf]

OK I can try to change the name of "GO terms enrich comparison (Human, Mouse, Rat)[clusterProfiler]", everything is up to date on github ?

==> Yes, in the "GO_terms_enrich_comparison" folder If you find the solution, please let me know ... !!

For "GO_terms_profiles_comparison", I think it was the first version of your tool @combesf, the one we did together when you came at Migale ?

==> yes it was indeed.

If that's the case we can delete it.

==> I agree.

(anyway we can still find it in github history)

[davidchristiany]

The .shed.yml is missing in "GO_terms_enrich_comparison": https://github.com/ifb-git/ProteoRE/tree/master/tools/GO_terms_enrich_comparison

@combesf Can you add it please ?

[combesf]

@davidchristiany done

[combesf]

I can put it on the testTS and mainTS, and install it on proteore-migale if you want ?

[davidchristiany]

I updated https://github.com/ifb-git/ProteoRE/tree/master/tools/GO_terms_enrich_comparison with the new name: Biological theme comparison

The problem you encountered was linked to the name in the .shed.yml: it was proteore_go_terms_profiles_comparison instead of proteore_go_terms_enrich_comparison

[combesf]

ok thanks for the info. I is my fault, sorry.

Do you or do I continue ?

[combesf]

ok I see it is updated on proteore-migale

[yvandenb]

Fixed by David