From 2af8b38b834c095711fd046773f476a0c442f957 Mon Sep 17 00:00:00 2001 From: Tapasweni Pathak Date: Tue, 7 Jun 2022 21:16:54 +0530 Subject: [PATCH 1/6] Address review comments by @greengypsy Ref: https://github.com/OpenMS/OpenMS-docs/pull/65. --- ...per-guidelines-for-addding-new-dependent-libraries.md | 8 ++++---- docs/additional-resources/external-code-using-openms.md | 2 +- docs/guides/user-guides/user-quickstart-guide.md | 2 +- docs/index.rst | 2 +- docs/tutorials/TOPP/TOPP-tutorial.md | 9 +++++---- docs/tutorials/TOPPAS/TOPPAS-tutorial.md | 6 +++--- docs/tutorials/TOPPAS/examples.md | 4 ++-- 7 files changed, 17 insertions(+), 16 deletions(-) diff --git a/docs/additional-resources/developer-guidelines-for-addding-new-dependent-libraries.md b/docs/additional-resources/developer-guidelines-for-addding-new-dependent-libraries.md index 7c16181f..47707d6e 100644 --- a/docs/additional-resources/developer-guidelines-for-addding-new-dependent-libraries.md +++ b/docs/additional-resources/developer-guidelines-for-addding-new-dependent-libraries.md @@ -25,17 +25,17 @@ with e.g. LGPL-2 would be prohibitive. ## C++ standard compatibility -Needs to be compatible and therefore compilable with the same C++ standard as OpenMS. +New dependency libraries needs to be compatible and therefore compilable with the same C++ standard as OpenMS. ## Availability for all platforms -OpenMS is meant to run and behave the same on the three main operating systems, i.e., Windows, macOS and Linux. Adding -a new dependent library is thus required to be available on these platforms +OpenMS has been designed for Windows, macOS, and Linux. Therefore, the new dependency library needs to be designed for +these platforms. - on **WindowsOS** this usually means, adding the new library to the Contrib in debug and release variants. In short all recent versions of Visual Studio (VS2008 and onwards) must be supported (or support must be added). This encompasses - a solution file (which can be either statically present or generated by a meta-system like CMake) is available - - the lib actually compiles and is linked to the **dynamic** VS-C++ runtime lib (since this is what the OpenMS lib will + - The library actually compiles and is linked to the **dynamic** VS-C++ runtime lib (since this is what the OpenMS lib will link to as well - combining static and dynamic links will lead to linker errors or segfaults). - on **macOS** it should be ensured that the library can be build on recent macOS versions (> 10.10) compiled using the diff --git a/docs/additional-resources/external-code-using-openms.md b/docs/additional-resources/external-code-using-openms.md index 5371faf8..fbdcb57f 100644 --- a/docs/additional-resources/external-code-using-openms.md +++ b/docs/additional-resources/external-code-using-openms.md @@ -103,7 +103,7 @@ If you've used an external project and have a new executable (+ an optional new well, and manually copy the new executable to the `TOPP/UTILS` binary directory (e.g. on Windows this could be `c:/program files/OpenMS/bin`, on Linux it could be `/bin`. -If you do NOT use the installer, copy all required files manually, plus a few extra steps, see below. What needs to be +If you do not use the installer, copy all required files manually, plus a few extra steps, see below. What needs to be done is a little platform dependent, thus very cumbersome to explain. Look at the cmake installer scripts, to see whats required (for Mac and Linux see `OpenMS/cmake/package*.cmake`). diff --git a/docs/guides/user-guides/user-quickstart-guide.md b/docs/guides/user-guides/user-quickstart-guide.md index b611400a..4e73e31b 100644 --- a/docs/guides/user-guides/user-quickstart-guide.md +++ b/docs/guides/user-guides/user-quickstart-guide.md @@ -31,7 +31,7 @@ Read the documentation of the tools see [TOPP tutorial](../../tutorials/TOPP/TOP Alternatively, use the command line and call tools directly. In this case, you'll probably want to use some type of shell script for automation. -## Adapte pipeline parameters +## Adapt pipeline parameters The default parameters of each tool can usually be tweaked to fit the data and improve results. diff --git a/docs/index.rst b/docs/index.rst index 740ae7a8..7d059105 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -17,7 +17,7 @@ quantitation, :term:`SILAC`, :term:`iTRAQ`, :term:`TMT`, :term:`SRM`, :term:`SWA It provides built-in algorithms for de-novo identification and database search, as well as adapters to other state-of-the art tools like X!Tandem, :term:`Mascot`, OMSSA, etc. It supports easy integration of OpenMS built tools into workflow -engines like :term:`KNIME`, Galaxy, WS-Pgrade, and :term:`TOPPAS` via the TOPPtools concept and +engines like :term:`KNIME`, Galaxy, WS-Pgrade, and :term:`TOPPAS` via the :term:`TOPP tools` concept and a unified parameter handling via a 'common tool description' (CTD) scheme. With :term:`pyOpenMS`, OpenMS offers Python bindings to a large part of the :term:`OpenMS API` diff --git a/docs/tutorials/TOPP/TOPP-tutorial.md b/docs/tutorials/TOPP/TOPP-tutorial.md index 90aea6f2..10e6ec9b 100644 --- a/docs/tutorials/TOPP/TOPP-tutorial.md +++ b/docs/tutorials/TOPP/TOPP-tutorial.md @@ -1,15 +1,16 @@ TOPP Tutorial ============ -This tutorial is an introduction to {term}`TOPP` and {term}`TOPPView`. Let's start with understanding the intent and +The following tutorial is an introduction to {term}`TOPP` and {term}`TOPPView`. Let's start with understanding the intent and concept of {term}`TOPP` compared to OpenMS. Later, we will move to the handling of {term}`TOPPView` which is our central GUI. Apart from viewing data, {term}`TOPPView` can also be used to analyze it using selected {term}`TOPP tools`; how-to is explained in the third part of the tutorial. + Finally, the tutorial lists the command line interfaces for all TOPP tools contained in the release. # Concepts -Let's understand the intent of [TOPP and OpenMS](topp-and-openms-introduction.md) in this part. +Let's understand the intent of [TOPP and OpenMS](topp-and-openms-introduction.md). ```{toctree} :maxdepth: 1 @@ -19,7 +20,7 @@ topp-and-openms-introduction # TOPPView Main Interface -In this part of the tutorial, we will learn about the main features of {term}`TOPPView` and its basic uses. +In the following section, we will learn about the main features of {term}`TOPPView` and its basic uses. ```{toctree} :maxdepth: 1 @@ -34,7 +35,7 @@ hotkeys-table # Calling TOPP tools from TOPPView -This part of the tutorial illustrates how to interactively analyse {term}`proteomics` data using {term}`TOPP tools` from +The following part of the tutorial illustrates how to interactively analyse {term}`proteomics` data using {term}`TOPP tools` from within {term}`TOPPView`. ```{toctree} diff --git a/docs/tutorials/TOPPAS/TOPPAS-tutorial.md b/docs/tutorials/TOPPAS/TOPPAS-tutorial.md index f44f47a7..b604804b 100644 --- a/docs/tutorials/TOPPAS/TOPPAS-tutorial.md +++ b/docs/tutorials/TOPPAS/TOPPAS-tutorial.md @@ -1,9 +1,9 @@ TOPPAS Tutorial ============== -**TOPPAS** allows to create, edit, open, save, and run TOPP workflows. Pipelines can be created conveniently in a GUI. -The parameters of all involved tools can be edited within TOPPAS and are also saved as part of the pipeline definition - in the `.toppas` file. +**TOPPAS** is a GUI tool that is used to create, edit, open, save, and run TOPP workflows. Pipelines can be created +conveniently in a GUI. The parameters of all involved tools can be edited within TOPPAS and are also saved as part of +the pipeline definition in the `.toppas` file. ```{toctree} :maxdepth: 1 diff --git a/docs/tutorials/TOPPAS/examples.md b/docs/tutorials/TOPPAS/examples.md index 9d42c732..ecec532d 100644 --- a/docs/tutorials/TOPPAS/examples.md +++ b/docs/tutorials/TOPPAS/examples.md @@ -17,8 +17,8 @@ TOPPView tutorial: [Smoothing raw data](../TOPP/smoothing-raw-data.md), [Subtrac ## Identification of E. coli peptides This section describes an example identification pipeline contained in the example directory, `Ecoli_Identification.toppas`. -It is shipped together with a reduced example mzML file containing 139 MS2 spectra from an E. coli run on an Orbitrap -instrument as well as an E. coli target-decoy database. +The pipeline is shipped together with a reduced example mzML file containing 139 MS2 spectra from an E. coli run on an +Orbitrap instrument as well as an E. coli target-decoy database. Use the search engine OMSSA (Geer et al., 2004) for peptide identification. Therefore, OMSSA must be installed and the path to the OMSSA executable (omssacl) must be set in the parameters of the OMSSAAdapter node. From f17e6f8f62f52e65380c98fc95198d016a4020c3 Mon Sep 17 00:00:00 2001 From: Tapasweni Pathak Date: Wed, 8 Jun 2022 16:30:11 +0530 Subject: [PATCH 2/6] add: exact syntax for adding admonition --- .github/CONTRIBUTING.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index ff30302a..90a7699e 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -31,7 +31,7 @@ For any questions, drop us a ping in [OpenMS Gitter](https://gitter.im/OpenMS/Op 6. Use `backtick`(s) for formatting code, library name, files, and path. 7. Use **bold** for product name, object name, an independent entity. 8. Use **bold** for menu title in an application. -9. Link to glossary terms using {term}`this is a glossary term`. +9. Link to glossary terms using {term}\`this is a glossary term\`. 10. OpenMS documentation uses following Admonitions - Hint - Important @@ -39,6 +39,7 @@ For any questions, drop us a ping in [OpenMS Gitter](https://gitter.im/OpenMS/Op - Warning - Tip - See Also + Example of these are present in documentation, please follow them. 11. Always specify lexers for code blocks. 12. Format keyboard strokes using `qwerty-keyboard-button`, as an example, please see [this](../docs/tutorials/TOPP/hotkeys-table.md) file. From 509a43be688005cc91cfd930eee47275e493bfde Mon Sep 17 00:00:00 2001 From: Tapasweni Pathak Date: Wed, 8 Jun 2022 16:37:26 +0530 Subject: [PATCH 3/6] add: soon to be deprecated important admonition for toppas --- docs/guides/user-guides/user-quickstart-guide.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/guides/user-guides/user-quickstart-guide.md b/docs/guides/user-guides/user-quickstart-guide.md index 4e73e31b..acbfd1cb 100644 --- a/docs/guides/user-guides/user-quickstart-guide.md +++ b/docs/guides/user-guides/user-quickstart-guide.md @@ -22,6 +22,12 @@ Before using OpenMS, become familiar with the following terms: |**TOPP tools** |A set of command line tools. Each of these command line tools is a building block of an analysis pipeline and are chained together in a way that fits the requirements of the user. The {term}`TOPP tools` are accessible from a command prompt/shell or via {term}`TOPPAS`. See also: [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md) and [TOPP documentation](../../topp/topp.md)| |**UTILS** |Similar to {term}`TOPP tools`, but with more supporting character, which are rarely used in a productive pipeline, but rather during pipeline construction or parameter optimization. See also: [UTILS documentation](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_documentation.html)| +```{important} +Users can now use {term}`KNIME` in place of {term}`TOPPAS`; the later will deprecated with no support in near future. +Please find more information about using {term}`KNIME` in [KNIME tutorial](../../tutorials/KNIME/KNIME-tutorial.md). +``` + + ## How to run a Tool A good start are the example pipelines (select **File** > **Open example file** within {term}`TOPPAS`). 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zO$LSx{cU-7S5-X%*5|-hHgNr|$kVo8pvoKEZ(?Ww`4Xvf4BFKN6hIb+^ze{`kvo21 zVFqwTiYyE<97!15^M=|95eBDkWMO1G!IeIyQ?~R>5IFSwGpC}B-1?0!zy(tfA5Mw6 zC=vtgIsUTZxYcdUa!UB+t5=JF?U4slfqS7^oD@$v&Ms_oSYY$(^7ZTPo{S6*)eFOF zf#ct9a~1-}*Dr+3NlZv+0Jda-7GBt6;oJcV6RVs#ib9+DSP(boVv17eC15mfnVK!#)Mn<~!4FCiTb}&q ZXE5`e736X8Vjqyt;OXk;vd$@?2>=+P(@+2a literal 0 HcmV?d00001 diff --git a/docs/tutorials/TOPP/toppview-introduction.md b/docs/tutorials/TOPP/toppview-introduction.md index 7ac5e984..9a266acf 100644 --- a/docs/tutorials/TOPP/toppview-introduction.md +++ b/docs/tutorials/TOPP/toppview-introduction.md @@ -11,3 +11,75 @@ datasets as well as displaying input data and output data of an algorithm togeth developers. ![TOPPView Parts](../../images/tutorials/topp/TOPPView_parts.png) + +The above example image shows a 2D view of TOPPView (blue rectangle) and the corresponding [Display modes and view options](display-modes-and-view-options.md) (red rectangle). The right dock area, shows the [Layers](#layers) (yellow rectangle), the [Spectrum browser](#spectrum-browser) (magenta rectangle) and the [Data filtering](data-filtering) (green rectangle). Switch between open windows can +be done using the tab bar (black rectangle). + +## Layers + +Each view of TOPPView supports several datasets, called layers. In the *layer manager* (dock window in the upper right +corner), layers can be hidden and shown using the check box in front of each layer name. + +By clicking on a layer, this layer is selected, which is indicated by a blue background. The selected layer can be +manipulated using the *Tools* menu. + +Layers can be copied by dragging them to the tab bar. If the layer is dropped on a tab, it is added to the corresponding +window. If the layer is dropped on the tab bar but not on a tab, a new window with that layer is added. + +## Spectrum browser + +The spectra contained in a peak map can be browsed in the *spectrum browser*. It displays a tree view of all spectra in +the current layer, where a spectrum with MS level *n* is a child of the spectrum with MS level *n - 1* that contains its +corresponding precursor peak. For each spectrum in the list, the retention time and (for spectra with MS level > 1) the +m/z value of the precursor peak are also shown. + +If a 2D or 3D window is active, double-clicking a spectrum will open it in a new 1D window. If the active window is a 1D +view, the spectra can be browsed and the currently selected spectrum will be shown. + +## Data filtering + +TOPPView allows filtering of the displayed peak data and feature data. Peak data can be filtered according to intensity +and meta data. Meta data is arbitrary data the peak is annotated with. Feature data can be filtered according to +intensity, charge, quality and meta data. + +Data filters are managed by a dock window. Filters can be added, removed and edited through the context menu (right +button mouse click) of the data filters window. For convenience, filters can also be edited by double-clicking them. + +## Command line options + +Several files can be opened in one layer from the command line by putting a '+' character between the file names. The +following command opens three files in three layers of the same window: + +```bash +TOPPView file1.mzML + file2.mzML + file3.mzML +``` + +Without the '+' the files would be opened in three different tabs. + +The color gradient used to display a file can be changed by adding one of several '@' commands. The following command +opens the file with a white-to-black gradient: + +```bash +TOPPView file1.mzML @bw +``` + +Automatic annotation of a layer with ID data (.osw files etc) can be performed by using the '!' character. This will +treat the next filename as annotation to the previous layer. The following command opens two layers in the same tab, +with the first layer being annotated: + +```bash +TOPPView file1.mzML ! file1.idXML + file2.mzML +``` + +For more information on command line parameters call: + +```bash +TOPPView --help +``` + +## Looking for help? + +You can display a short help text for each button and dock window of TOPPView by clicking on it in *What's this?* mode. +*What's this?* mode can be entered using the *Help* menu. + +![](../../images/tutorials/topp/TOPPView_help.png) From 025faeaa831b2c8510bc9011e4754458fc69f27c Mon Sep 17 00:00:00 2001 From: Tapasweni Pathak Date: Fri, 10 Jun 2022 17:56:12 +0530 Subject: [PATCH 5/6] prettier: ui enhancements Fixes https://github.com/OpenMS/OpenMS-docs/issues/66. Fixes https://github.com/OpenMS/OpenMS-docs/issues/71. Closes https://github.com/OpenMS/OpenMS-docs/issues/79. Fixes https://github.com/OpenMS/OpenMS-docs/issues/81. --- conf.py | 10 ++++ docs/contact-us.md | 2 +- docs/glossary.md | 3 -- .../user-guides/user-quickstart-guide.md | 13 +++-- docs/index.rst | 4 +- .../installation-on-gnu-linux.md | 44 +++++++++-------- docs/introduction.md | 13 +++++ .../adding-new-tool-to-topp.md | 0 .../ini-file-editor.md | 0 docs/topp-and-utils/proteomicslfq.md | 49 +++++++++++++++++++ docs/{topp => topp-and-utils}/swathwizard.md | 0 .../topp-and-utils.md} | 24 ++++++++- docs/{topp => topp-and-utils}/toppas.md | 0 docs/{topp => topp-and-utils}/toppview.md | 0 .../TOPP/display-modes-and-view-options.md | 4 +- .../TOPP/peptide-property-prediction.md | 2 +- docs/tutorials/TOPP/picking-peaks.md | 2 +- .../tutorials/TOPP/profile-data-processing.md | 4 +- 18 files changed, 136 insertions(+), 38 deletions(-) rename docs/{topp => topp-and-utils}/adding-new-tool-to-topp.md (100%) rename docs/{topp => topp-and-utils}/ini-file-editor.md (100%) create mode 100644 docs/topp-and-utils/proteomicslfq.md rename docs/{topp => topp-and-utils}/swathwizard.md (100%) rename docs/{topp/topp.md => topp-and-utils/topp-and-utils.md} (61%) rename docs/{topp => topp-and-utils}/toppas.md (100%) rename docs/{topp => topp-and-utils}/toppview.md (100%) diff --git a/conf.py b/conf.py index 0524eee0..e7f0afde 100644 --- a/conf.py +++ b/conf.py @@ -36,6 +36,16 @@ 'sphinx_inline_tabs', ] +myst_enable_extensions = [ + "tasklist", + "dollarmath", + "amsmath", + "colon_fence", + "linkify", + "replacements", + "linkify_fuzzy_links", +] + autosummary_generate = True autosummary_imported_members = True diff --git a/docs/contact-us.md b/docs/contact-us.md index 3f450fd3..6d3cc82c 100644 --- a/docs/contact-us.md +++ b/docs/contact-us.md @@ -1,7 +1,7 @@ Contact Us ========= -Join us on [Discord](https://discord.com/invite/swkxs72CHB)! +Join us on [Discord](https://discord.gg/WxynEEsf5X)! You can also contact us: diff --git a/docs/glossary.md b/docs/glossary.md index e3f2eb48..764ae707 100644 --- a/docs/glossary.md +++ b/docs/glossary.md @@ -102,9 +102,6 @@ Collision-induced dissociation (CID) TOPP The OpenMS Proteomics Pipeline. -TOPPAS.app - TOPPAS allows to create, edit, open, save, and run TOPP workflows. - MSGFPlusAdapter Adapter for the MS-GF+ protein identification (database search) engine. More information is available [here](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_MSGFPlusAdapter.html). diff --git a/docs/guides/user-guides/user-quickstart-guide.md b/docs/guides/user-guides/user-quickstart-guide.md index 5293ab1b..71d07e42 100644 --- a/docs/guides/user-guides/user-quickstart-guide.md +++ b/docs/guides/user-guides/user-quickstart-guide.md @@ -19,8 +19,13 @@ Before using OpenMS, become familiar with the following terms: |--------------------|-------------| |**TOPPView** |A tool that is used to view and explore {term}`LC-MS` data, alignments, groups, peptide identifications, and more.| |**TOPPAS** |A graphical workflow design tool that is used to create pipelines from all {term}`TOPP tools` (and {term}`UTILS`).| -|**TOPP tools** |A set of command line tools. Each of these command line tools is a building block of an analysis pipeline and are chained together in a way that fits the requirements of the user. The {term}`TOPP tools` are accessible from a command prompt/shell or via {term}`TOPPAS`. See also: [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md) and [TOPP documentation](../../topp/topp.md)| -|**UTILS** |Similar to {term}`TOPP tools`, but with more supporting character, which are rarely used in a productive pipeline, but rather during pipeline construction or parameter optimization. See also: [UTILS documentation](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_documentation.html)| +|**TOPP tools** |A set of command line tools. Each of these command line tools is a building block of an analysis pipeline and are chained together in a way that fits the requirements of the user. The {term}`TOPP tools` are accessible from a command prompt/shell or via {term}`TOPPAS`. See also: [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md) and [TOPP documentation](../../topp-and-utils/topp-and-utils.md)| +|**UTILS** |Besides {term}`TOPP`, OpenMS offers range of other tools. They are not included in {term}`TOPP` as they are not part of typical analysis pipelines. A set of command line utilities, similar to {term}`TOPP tools`, mostly used during pipeline construction or parameter optimization. | + +```{seealso} + +[UTILS documentation](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_documentation.html)| +``` ```{important} Users can now use {term}`KNIME` in place of {term}`TOPPAS`; the later will deprecated with no support in near future. @@ -32,7 +37,7 @@ Please find more information about using {term}`KNIME` in [KNIME tutorial](../.. A good start are the example pipelines (select **File** > **Open example file** within {term}`TOPPAS`). -Read the documentation of the tools see [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md), [TOPP documentation](../../topp/topp.md) and the one of ([TOPPAS tutorial](../../tutorials/TOPPAS/TOPPAS-tutorial.md)). +Read the documentation of the tools see [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md), [TOPP documentation](../../topp-and-utils/topp-and-utils.md) and the one of ([TOPPAS tutorial](../../tutorials/TOPPAS/TOPPAS-tutorial.md)). Alternatively, use the command line and call tools directly. In this case, you'll probably want to use some type of shell script for automation. @@ -54,7 +59,7 @@ The default parameters of each tool can usually be tweaked to fit the data and i e.g. `FileFilter -write_ini filefilter.ini` - Now, edit the INI file (which is a XML file) using the [INIFileEditor](../../topp/ini-file-editor.md), which is another GUI tool shipped with + Now, edit the INI file (which is a XML file) using the [INIFileEditor](../../topp-and-utils/ini-file-editor.md), which is another GUI tool shipped with OpenMS and similar to the one build into {term}`TOPPAS`. ### How do I feed the INI file to a Tool? diff --git a/docs/index.rst b/docs/index.rst index eb92fa7a..60195449 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -71,8 +71,8 @@ Contents :maxdepth: 2 :caption: OpenMS TOPP Tools - topp/topp.md - topp/adding-new-tool-to-topp.md + topp-and-utils/topp-and-utils.md + topp-and-utils/adding-new-tool-to-topp.md .. toctree:: :maxdepth: 2 diff --git a/docs/installations/installation-on-gnu-linux.md b/docs/installations/installation-on-gnu-linux.md index f6482b31..0da62ce9 100644 --- a/docs/installations/installation-on-gnu-linux.md +++ b/docs/installations/installation-on-gnu-linux.md @@ -5,16 +5,6 @@ Installation on GNU/Linux Use conda or bioconda to install OpenMS. -1. Follow the instructions to [install conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html). -2. Install OpenMS using conda: - `conda install -c openms openms` -3. Other OpenMS packages can be installed using: - ``` - conda install -c openms pyopenms - conda install -c openms openms-thirdparty - conda install -c openms libopenms - ``` - ```{tab} openms openms contains OpenMS C++ Tools. ``` @@ -32,6 +22,16 @@ openms-thirdparty are external tools that are wrapped in OpenMS with adapters. T the openms package. ``` +1. Follow the instructions to [install conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html). +2. Install OpenMS using conda: + `conda install -c openms openms` +3. Other OpenMS packages can be installed using: + ``` + conda install -c openms pyopenms + conda install -c openms openms-thirdparty + conda install -c openms libopenms + ``` + To install using bioconda: ``` @@ -85,13 +85,8 @@ These packages are not directly maintained by the OpenMS team and they can not b same behaviour as when building it from source code. Also, their availability and version is subject to change and support might be limited (due to unforeseen or untested behaviour). It is suggested not to install them parallel to our Debian package. - ``` -## Installation via building from source code - -The source code of OpenMS is available on GitHub. Follow [Building OpenMS on GNU/Linux](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/install_linux.html) instructions on how to build OpenMS from source. - ```{note} Some thirdparty software used via adapter tools in OpenMS might also require an installed JavaVM. ``` @@ -102,8 +97,17 @@ Make sure you have [Docker installed](https://docs.docker.com/engine/install/). Our Docker support is constantly updated. Images can be obtained via [ghcr.io](https://ghcr.io). -1. [openms-executables](https://ghcr.io/openms/openms-executables:latest) -2. [openms-library](https://ghcr.io/openms/openms-library:latest) +```{tab} + +[openms-executables](https://ghcr.io/openms/openms-executables:latest) + +``` + +```{tab} + +[openms-library](https://ghcr.io/openms/openms-library:latest) + +``` Or via [BioContainers Registeries](https://biocontainers.pro/registry). @@ -116,9 +120,9 @@ Docker images can be pulled via or one of the following commands: ``` docker pull biocontainers/openms -docker pull openms/library -docker pull openms/executables -docker pull openms/pyopenms +docker pull biocontainers/libopenms +docker pull biocontainers/openms-thirdparty +docker pull biocontainers/pyopenms ``` Dockerfiles to build different kind of images (corresponding to build instructions, e.g. on ArchLinux) can be found on diff --git a/docs/introduction.md b/docs/introduction.md index 324089e2..c8d6ef45 100644 --- a/docs/introduction.md +++ b/docs/introduction.md @@ -94,13 +94,26 @@ Get started with installing OpenMS using the installers available for different ## Installation on different platforms ```{tab} GNU/Linux + +```bash wget https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/OpenMS-2.8.0-Debian-Linux-x86_64.deb + +``` + ``` ```{tab} Windows + +```bash wget https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/OpenMS-2.8.0-Win64.exe ``` +``` + ```{tab} macOS + +```bash wget https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/OpenMS-2.8.0-macOS.dmg ``` + +``` diff --git a/docs/topp/adding-new-tool-to-topp.md b/docs/topp-and-utils/adding-new-tool-to-topp.md similarity index 100% rename from docs/topp/adding-new-tool-to-topp.md rename to docs/topp-and-utils/adding-new-tool-to-topp.md diff --git a/docs/topp/ini-file-editor.md b/docs/topp-and-utils/ini-file-editor.md similarity index 100% rename from docs/topp/ini-file-editor.md rename to docs/topp-and-utils/ini-file-editor.md diff --git a/docs/topp-and-utils/proteomicslfq.md b/docs/topp-and-utils/proteomicslfq.md new file mode 100644 index 00000000..55bd1122 --- /dev/null +++ b/docs/topp-and-utils/proteomicslfq.md @@ -0,0 +1,49 @@ +ProteomicsLFQ +============= + + +ProteomicsLFQ performs label-free quantification of peptides and proteins. + +## Input + +- Spectra in mzML format +- Identifications in idXML or mzIdentML format with posterior error probabilities as score type. To generate those we + suggest to run: + - PeptideIndexer to annotate target and decoy information. + - PSMFeatureExtractor to annotate percolator features. + - PercolatorAdapter tool (score_type = 'q-value', -post-processing-tdc). + - IDFilter (pep:score = 0.01) to filter PSMs at 1% FDR. +- An experimental design file: + + ```{seealso} + [Experimental Design](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/classOpenMS_1_1ExperimentalDesign.html) for details. + ``` +- A protein database in with appended decoy sequences in FASTA format. + (e.g., generated by the [OpenMS DecoyDatabase tool](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/namespaceOpenMS.html)). + Processing: + ProteomicsLFQ has different methods to extract features: ID-based (targeted only), or both ID-based and untargeted. + - The first method uses targeted feature dectection using RT and m/z information derived from identification data to + extract features. + ```{note} + Only identifications found in a particular MS run are used to extract features in the same run. No transfer of IDs + (match between runs) is performed. + ``` + - The second method adds untargeted feature detection to obtain quantities from unidentified features. Transfer of Ids + (match between runs) is performed by transfering feature identifications to coeluting, unidentified features with + similar mass and RT in other runs. + +## Requantification + +Optionally, a requantification step is performed that tries to fill NA values. If a peptide has been quantified in +more than half of all maps, the peptide is selected for requantification. In that case, the mean observed RT +(and theoretical m/z) of the peptide is used to perform a second round of targeted extraction. + +## Output + +Output format are as follows: + +- mzTab file with analysis results. +- MSstats file with analysis results for statistical downstream analysis in MSstats. +- ConsensusXML file for visualization and further processing in OpenMS. + +Potential scripts to perform the search can be found under `src/tests/topp/ProteomicsLFQTestScripts`. diff --git a/docs/topp/swathwizard.md b/docs/topp-and-utils/swathwizard.md similarity index 100% rename from docs/topp/swathwizard.md rename to docs/topp-and-utils/swathwizard.md diff --git a/docs/topp/topp.md b/docs/topp-and-utils/topp-and-utils.md similarity index 61% rename from docs/topp/topp.md rename to docs/topp-and-utils/topp-and-utils.md index 7309d620..23f0d78e 100644 --- a/docs/topp/topp.md +++ b/docs/topp-and-utils/topp-and-utils.md @@ -1,5 +1,5 @@ TOPP -=== +==== **TOPP - The OpenMS Proteomics Pipeline** is a pipeline for the analysis of HPLC-MS data. It consists of several small applications that can be chained to create analysis pipelines tailored for a specific problem. @@ -20,3 +20,25 @@ swathwizard ``` For advanced documentation on every TOPP tool, see the [OpenMS TOPP API Reference](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_documentation.html). + +UTILS +===== + +Besides {term}`TOPP`, OpenMS offers range of other tools. They are not included in {term}`TOPP` as they are not part of +typical analysis pipelines. A set of command line utilities, similar to {term}`TOPP tools`, mostly used during pipeline +construction or parameter optimization. + + +```{seealso} + +[UTILS documentation](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_documentation.html) + +``` + +Let's explore one such utitliy tool: + +```{toctree} +:maxdepth: 1 + +proteomicslfq +``` diff --git a/docs/topp/toppas.md b/docs/topp-and-utils/toppas.md similarity index 100% rename from docs/topp/toppas.md rename to docs/topp-and-utils/toppas.md diff --git a/docs/topp/toppview.md b/docs/topp-and-utils/toppview.md similarity index 100% rename from docs/topp/toppview.md rename to docs/topp-and-utils/toppview.md diff --git a/docs/tutorials/TOPP/display-modes-and-view-options.md b/docs/tutorials/TOPP/display-modes-and-view-options.md index 503d3c41..75b4eac6 100644 --- a/docs/tutorials/TOPP/display-modes-and-view-options.md +++ b/docs/tutorials/TOPP/display-modes-and-view-options.md @@ -6,7 +6,7 @@ Display modes determine how intensities are displayed. View options configure th ![TOPPView Icons](../../images/tutorials/topp/TOPPView_icons.png) -# Display Modes +## Display Modes Intensity display modes determine the way peak intensities are displayed. @@ -24,7 +24,7 @@ opened it corresponds to the normal mode. In this mode the maximum currently displayed intensity is treated as if it was the maximum overall intensity. -# View Options +## View Options View options configure the view of the current layer. diff --git a/docs/tutorials/TOPP/peptide-property-prediction.md b/docs/tutorials/TOPP/peptide-property-prediction.md index 1406e81f..c46ec173 100644 --- a/docs/tutorials/TOPP/peptide-property-prediction.md +++ b/docs/tutorials/TOPP/peptide-property-prediction.md @@ -1,7 +1,7 @@ Peptide Property Prediction =========================== -You can train a model for retention time prediction as well as for the prediction of proteotypic peptides. +Train a model for retention time prediction as well as for the prediction of proteotypic peptides. Two applications has been described in the following publications: Nico Pfeifer, Andreas Leinenbach, Christian G. Huber and Oliver Kohlbacher Statistical learning of peptide retention behavior in chromatographic separations: A new diff --git a/docs/tutorials/TOPP/picking-peaks.md b/docs/tutorials/TOPP/picking-peaks.md index b31845b4..8a00b905 100644 --- a/docs/tutorials/TOPP/picking-peaks.md +++ b/docs/tutorials/TOPP/picking-peaks.md @@ -13,7 +13,7 @@ the approximate `fwhm` of peaks, use the estimation included in the PeakPickerWa to `true`. After applying the PeakPickerWavelet, observe which peak width was estimated and used for peak picking in the log window. -To estimate the peak width, use the measuring tool ([Action Modes and Their Uses](views-in-toppview.md##action-modes-and-their-uses)) to determine +To estimate the peak width, use the measuring tool ([Action Modes and Their Uses](views-in-toppview.md#action-modes-and-their-uses)) to determine the fwhm of one or several representative peaks. If the peak picker delivers only a few peaks even though the `peak_with` and `signal_to_noise` parameters are set to diff --git a/docs/tutorials/TOPP/profile-data-processing.md b/docs/tutorials/TOPP/profile-data-processing.md index 55340593..7c45c122 100644 --- a/docs/tutorials/TOPP/profile-data-processing.md +++ b/docs/tutorials/TOPP/profile-data-processing.md @@ -51,9 +51,7 @@ Please notice that this method is still **experimental** since it has not been t See the `PeakPickerHiRes` class documentation for a parameter list. -## Finding the right parameters for the - -NoiseFilters, the BaselineFilter and the PeakPickers +## Finding the right parameters for the NoiseFilters, the BaselineFilter and the PeakPickers Finding the right parameters is not trivial. The default parameters will not work on most datasets. In order to find good parameters, following this procedure: From a940f0a59e56710881478fe239e674eaf02670c5 Mon Sep 17 00:00:00 2001 From: Tapasweni Pathak Date: Fri, 10 Jun 2022 17:53:34 +0530 Subject: [PATCH 6/6] fixes: merge conflicts --- docs/tutorials/TOPP/toppview-introduction.md | 85 -------------------- 1 file changed, 85 deletions(-) delete mode 100644 docs/tutorials/TOPP/toppview-introduction.md diff --git a/docs/tutorials/TOPP/toppview-introduction.md b/docs/tutorials/TOPP/toppview-introduction.md deleted file mode 100644 index 9a266acf..00000000 --- a/docs/tutorials/TOPP/toppview-introduction.md +++ /dev/null @@ -1,85 +0,0 @@ -TOPPView Introduction -===================== - -{term}`TOPPView` is a viewer for {term}`MS` and {term}`HPLC-MS` data. It can be used to inspect files in {term}`mzML`, -{term}`mzData`, {term}`mzXML` and several other text-based file formats. - -In each view, several datasets can be displayed using the layer concept. This allows visual comparison of several -datasets as well as displaying input data and output data of an algorithm together. - -{term}`TOPPView` is intended for visual inspection of the data by experimentalists as well as for analysis software by -developers. - -![TOPPView Parts](../../images/tutorials/topp/TOPPView_parts.png) - -The above example image shows a 2D view of TOPPView (blue rectangle) and the corresponding [Display modes and view options](display-modes-and-view-options.md) (red rectangle). The right dock area, shows the [Layers](#layers) (yellow rectangle), the [Spectrum browser](#spectrum-browser) (magenta rectangle) and the [Data filtering](data-filtering) (green rectangle). Switch between open windows can -be done using the tab bar (black rectangle). - -## Layers - -Each view of TOPPView supports several datasets, called layers. In the *layer manager* (dock window in the upper right -corner), layers can be hidden and shown using the check box in front of each layer name. - -By clicking on a layer, this layer is selected, which is indicated by a blue background. The selected layer can be -manipulated using the *Tools* menu. - -Layers can be copied by dragging them to the tab bar. If the layer is dropped on a tab, it is added to the corresponding -window. If the layer is dropped on the tab bar but not on a tab, a new window with that layer is added. - -## Spectrum browser - -The spectra contained in a peak map can be browsed in the *spectrum browser*. It displays a tree view of all spectra in -the current layer, where a spectrum with MS level *n* is a child of the spectrum with MS level *n - 1* that contains its -corresponding precursor peak. For each spectrum in the list, the retention time and (for spectra with MS level > 1) the -m/z value of the precursor peak are also shown. - -If a 2D or 3D window is active, double-clicking a spectrum will open it in a new 1D window. If the active window is a 1D -view, the spectra can be browsed and the currently selected spectrum will be shown. - -## Data filtering - -TOPPView allows filtering of the displayed peak data and feature data. Peak data can be filtered according to intensity -and meta data. Meta data is arbitrary data the peak is annotated with. Feature data can be filtered according to -intensity, charge, quality and meta data. - -Data filters are managed by a dock window. Filters can be added, removed and edited through the context menu (right -button mouse click) of the data filters window. For convenience, filters can also be edited by double-clicking them. - -## Command line options - -Several files can be opened in one layer from the command line by putting a '+' character between the file names. The -following command opens three files in three layers of the same window: - -```bash -TOPPView file1.mzML + file2.mzML + file3.mzML -``` - -Without the '+' the files would be opened in three different tabs. - -The color gradient used to display a file can be changed by adding one of several '@' commands. The following command -opens the file with a white-to-black gradient: - -```bash -TOPPView file1.mzML @bw -``` - -Automatic annotation of a layer with ID data (.osw files etc) can be performed by using the '!' character. This will -treat the next filename as annotation to the previous layer. The following command opens two layers in the same tab, -with the first layer being annotated: - -```bash -TOPPView file1.mzML ! file1.idXML + file2.mzML -``` - -For more information on command line parameters call: - -```bash -TOPPView --help -``` - -## Looking for help? - -You can display a short help text for each button and dock window of TOPPView by clicking on it in *What's this?* mode. -*What's this?* mode can be entered using the *Help* menu. - -![](../../images/tutorials/topp/TOPPView_help.png)