Ordering of sections

[jpfeuffer]

We should probably think about the order of the doc sections. I just looked at the headings in the Sidebar and I felt like the order is not always optimal. E.g. TOPP tools are explained after the TOPP Tutorial. And Scripting with TOPP might be better suited in the TOPP section.

Read Existing Documentation

I have checked the following places for the error:

• [ ] [OpenMS Documentation Troubleshooting]()
• [ ] [OpenMS API Developer FAQs]()

Create OpenMS Bug Report

I have created the bug report in OpenMS for any pipeline errors.

• [ ] OpenMS Open Issues

Description of the documentation bug

• [ ] I have attached screenshots of the incorrect documentation

Expected behaviour

OpenMS Installation

• Version:

Additional context

[tapaswenipathak]

TOPP tools are explained after the TOPP Tutorial

In terms of content for readers TOPP Tutorial has more advanced and informative content than TOPP Tools.

OpenMS TOPP tools just give an introduction and a redirect to API reference. I would say -1.

And Scripting with TOPP might be better suited in the TOPP section.

The focus for users is TOPP Tutorial and not TOPP section. Do it in one go or together as we have parallel equal weightage focus point for readers in API reference. -1.

[greengypsy]

I agree with @jpfeuffer. I think that the tutorials should go after the tools description section. This is an example:

[greengypsy]

ntroduction

What is OpenMS Background Getting Started

Installation on GNU/Linux Installation on macOS Installation on Windows Quick Start Guides

User Quick Start Guide Contributor Quick Start Guide TOPP

What is TOPP Key Concepts TOP tools Graphical tools File handling tools Signal processing and preprocessing tools Quanitation tools Map Alignment tools Protein/Peptide identification tools etc KNIME

What is KNIME User interface Examples TOPPAS

What is TOPPAS User Interface Examples Tutorials

TOPP KNIME TOPPAS Developer Resources

Developer guidelines for adding new dependency libraries Link external code to OpenMS Custom compilation of OpenMS Build custom KNIME application Add new tool to the TOP suite Additional Resources

OpenMS git workflow Reporting bugs and issues Write and label github issues Pull request checklist Downloads

OpenMS installers Workflows OpenMS releases Other resources Quick Reference

Contributor FAQ Developer FAQ Glossary Contact Us

[timosachsenberg]

@jpfeuffer @greengypsy do you think it would make sense to put this into a "workflow system" section? e.g., we will probably expand this with nextflow, snakemake and galaxy in the future. Having a top level menu entry for all of them seems a bit overkill

What is KNIME User interface Examples TOPPAS

What is TOPPAS User Interface Examples Tutorials

[tapaswenipathak]

Introduction​​

• [ ] ## About OpenMS
• [ ] ## Background
• [ ] ## How OpenMS Works

Getting Started

• [ ] ## Installation on GNU/Linux
• [ ] ## Installation on macOS
• [ ] ## Installation on Windows

OpenMS Applications and Tools

• [ ] ## OpenMS Application

• [ ] ## TOPP Tools

• [ ] ### Introduction to TOPP

• [ ] ### Key Concepts

• [ ] ### Types of TOPP tools

• [ ] - Graphical tools

• [ ] - File handling tools

• [ ] - Signal processing and preprocessing tools

• [ ] - Quantitation tools

• [ ] - Map Alignment tools

• [ ] - Protein/Peptide identification tools

• [ ] ## UTILS Tools

• [ ] ### Introduction to UTILS

• [ ] ### Key Concepts

• [ ] ### Types of TOPP tools

• [ ] ## Command Line Interface

• [ ] ## Visualize with OpenMS

Run workflows with OpenMS Tools

OpenMS in KNIME

(introduction): not a heading

• [ ] ### Installation
• [ ] ### Getting started
• [ ] ### Workflows (link to downloads)

OpenMS in nextflow

(introduction): not a heading

• [ ] ### Installation
• [ ] ### Getting started
• [ ] ### Workflows (link to downloads)

OpenMS on Galaxy

(introduction): not a heading

• [ ] ### Installation
• [ ] ### Getting started
• [ ] ### Workflows (link to downloads)

Tutorials and Quick Start Guides

Tutorials

• [ ] ### TOPPView Tut

• [ ] ### TOPP Shell tut

• [ ] ### User tut

Quick Stat guides

• [ ] ### KNIME qsg
• [ ] ### Nextflow qsg
• [ ] ### Galaxy qsg
• [ ] ### Developer
• [ ] ### Contributor
• [ ] ### User

Develop with OpenMS

• [ ] ## C++
• [ ] ## Python
• [ ] ## OpenMS Core Library
• [ ] ## Build OpenMS from source
• [ ] ## Link external code to OpenMS
• [ ] ## Developer tutorial (external/doxygen)
• [ ] ## API reference (external/doxygen)

Contribute to OpenMS

• [ ] ## Build from Source
• [ ] ## OpenMS Git Workflow
• [ ] ## Add new tool to the TOPP suite
• [ ] ## Pull request checklist
• [ ] ## Reporting bugs and issues (and how to label them)

Advanced

• [ ] ### Developer guidelines for adding new dependency libraries
• [ ] ### Build custom KNIME plugin

Downloads

• [ ] ## OpenMS installers

• [ ] ## Workflows

• [ ] ## OpenMS releases

• [ ] ## Other resources

• [ ] ### Schema

• [ ] ### Data

• [ ] ### Tutorials/Guides

• [ ] ### Scripts

Quick Reference

• [ ] ## Contributor FAQ
• [ ] ## Developer FAQ
• [ ] ## Contact Us
• [ ] ## Glossary

cc @greengypsy.

(the doc has limited visibility restrictions)

Deps

• https://github.com/OpenMS/Tutorials/issues/205.

[tapaswenipathak]

cc @axelwalter @enetz @jpfeuffer @KyowonJeong @poshul @OpenMS/doc-team.

Please feel free to add comments/suggestions/thoughts/edits on finalized structure for the first iteration.

while i and @christinakumar prep for merge.

[enetz]

I feel like we can leave out the Utils section? In practice the Utils are just TOPP tools, same interface, same user experience. They are just usually in beta and less well tested. A sub-page under TOPP Tools describing that should be enough.