From 0a8a1af73a860764b3e9afd59811c110cf9c50f9 Mon Sep 17 00:00:00 2001 From: Tapasweni Pathak Date: Tue, 24 May 2022 17:42:05 +0530 Subject: [PATCH 1/2] Fixes: review comments by @greengypsy --- .github/CONTRIBUTING.md | 16 +++++----- docs/contact-us.md | 8 ++--- .../user-guides/user-quickstart-guide.md | 22 ++++++------- docs/index.rst | 7 ++-- docs/introduction.md | 4 +-- docs/topp/ini-file-editor.md | 2 +- docs/topp/swathwizard.md | 4 +-- docs/topp/toppas.md | 6 ++-- docs/topp/toppview.md | 4 +-- .../TOPP/consensus-peptide-identification.md | 3 +- .../TOPP/data-analysis-in-toppview.md | 8 ++--- .../TOPP/display-modes-and-view-options.md | 2 +- .../feature-detection-on-centroided-data.md | 2 +- docs/tutorials/TOPP/feature-grouping.md | 4 +-- docs/tutorials/TOPP/general-introduction.md | 2 +- docs/tutorials/TOPP/map-alignment.md | 2 +- docs/tutorials/TOPP/picking-peaks.md | 2 +- .../tutorials/TOPP/profile-data-processing.md | 4 +-- docs/tutorials/TOPP/quality-control.md | 2 +- .../subtracting-a-baseline-from-a-spectrum.md | 9 +++--- docs/tutorials/TOPP/toppview-introduction.md | 2 +- docs/tutorials/TOPP/views-in-toppview.md | 6 ++-- docs/tutorials/TOPPAS/examples.md | 24 +++++++------- docs/tutorials/TOPPAS/general-introduction.md | 2 +- docs/tutorials/TOPPAS/user-interface.md | 32 +++++++++---------- 25 files changed, 91 insertions(+), 88 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 14296434..5acbdaa7 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -5,14 +5,14 @@ Hi there! Thank you for thinking about enhancing OpenMS Documentation further. -Please feel free: +Please feel free to: -1. Creating a bug report or feature request in OpenMS Documentation, [here](https://github.com/OpenMS/OpenMS-docs/issues). -2. Creating a pull request in [OpenMS Documentation](https://github.com/OpenMS/OpenMS-docs) with the change you're proposing. +1. Create a bug report or feature request in OpenMS Documentation, [here](https://github.com/OpenMS/OpenMS-docs/issues). +2. Create a pull request in [OpenMS Documentation](https://github.com/OpenMS/OpenMS-docs) with the change you're proposing. -If you need help while doing any of these, drop us a ping in [OpenMS Gitter](https://gitter.im/OpenMS/OpenMS). +For any questions, drop us a ping in [OpenMS Gitter](https://gitter.im/OpenMS/OpenMS). -## Creating a Pull Request +## Create a Pull Request(PR) 1. Fork this repository. 2. Add the change in your fork. @@ -36,13 +36,13 @@ If you need help while doing any of these, drop us a ping in [OpenMS Gitter](htt ### Images and figures -For images and figures, follow: +For images and figures: -1. Add screenshot of the window. +1. Add a screenshot of the window. 2. In tutorial, align images in center. Other instructions, should have alighment to left. 3. Please set the size to `500px` of images added in step-by-step guides or instructions. -## OpenMS Documentation Contributors +## OpenMS documentation contributors Thank you for your contribution! diff --git a/docs/contact-us.md b/docs/contact-us.md index 07c4c860..b78a4079 100644 --- a/docs/contact-us.md +++ b/docs/contact-us.md @@ -1,14 +1,14 @@ Contact Us ========= -To get in touch with us, please follow preferred medium/channel as listed below: +Contact us: -1. For [user and contributor real time Gitter chat](https://gitter.im/OpenMS/OpenMS). +1. Using the user and contributor real time [Gitter chat](https://gitter.im/OpenMS/OpenMS). 2. Drop us an email at user support [open-ms-general](https://sourceforge.net/projects/open-ms/lists/open-ms-general) mailing list. 3. To stay updated of new versions of OpenMS and releases, subscribe to [openms-announcements mailing list](https://sourceforge.net/projects/open-ms/lists/open-ms-announcements). -4. In ordered to report a new bug, please create an issue on GitHub [OpenMS](https://github.com/OpenMS/OpenMS/issues) +4. In order to report a new bug, please create an issue on GitHub [OpenMS](https://github.com/OpenMS/OpenMS/issues) repository. -Say hi, on [OpenMS Twitter](https://twitter.com/openmsteam)! +Say hi on [OpenMS Twitter](https://twitter.com/openmsteam)! diff --git a/docs/guides/user-guides/user-quickstart-guide.md b/docs/guides/user-guides/user-quickstart-guide.md index 9f77a5f2..8bd0ea8a 100644 --- a/docs/guides/user-guides/user-quickstart-guide.md +++ b/docs/guides/user-guides/user-quickstart-guide.md @@ -13,7 +13,7 @@ under the three clause BSD licence and runs under Windows, macOS, and Linux oper ## Background -Before using [OpenMS.org](https://www.openms.de/), you need to be familiar with the following terms: +Before using OpenMS, become familiar with the following terms: | Tool and Utilities | Description | |--------------------|-------------| @@ -24,17 +24,18 @@ Before using [OpenMS.org](https://www.openms.de/), you need to be familiar with ## How to run a Tool -It is recommended to use TOPPAS. A good start are the example pipelines (select **File** > **Open example file** within TOPPAS). -In parallel read the documentation of the tools (see [TOPP tutorial](), [TOPP documentation](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_documentation.html)) and the one of TOPPAS ([TOPPAS tutorial](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_documentation.html)). +A good start are the example pipelines (select **File** > **Open example file** within TOPPAS). -Alternatively, you can use the command line and call tools directly. In this case you'll probably want to use some type of shell +Read the documentation of the tools (see [TOPP tutorial](), [TOPP documentation](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_documentation.html)) and the one of TOPPAS ([TOPPAS tutorial](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_documentation.html)). + +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. -## Adapting your Pipeline Parameters +## Adapting your pipeline parameters The default parameters of each tool can usually be tweaked to fit the data and improve results. -### Where do you change them? +### Where do you change pipeline parameters? 1. **TOPPAS**: Double-click the node of which you want to change the parameters of. A short docu for each parameter will show up once it is selected. All parameters which would be available on the command line and in the INI @@ -54,13 +55,12 @@ The default parameters of each tool can usually be tweaked to fit the data and i 1. **TOPPAS**: Once you changed the parameters of a node and clicked **Ok**, the parameters are in effect. Because they are part of the TOPPAS workflow, they are saved together with the workflow. -2. **Command line** : Simply supply the INI file via the `-ini` flag, +2. **Command line** : Supply the INI file via the `-ini` flag, ` -ini ` e.g. `FileFilter -ini filefilter.ini` -### What parameters require to be changed and to what value? +### What parameters to set and to what value? -This is tricky and its not possible to give a general answer. In general, read the tool description, change the -parameters and compare the results using TOPPView if possible. If that does not help, drop us an email on the -[OpenMS mailing list]() and ask. Please include all the necessary details we need in order to help you. +The answer is complex, in general, read the tool description, change the parameters and compare the results using +TOPPView if possible. If that does not help, [contact us](../../contact-us.md). Please include all the necessary details we need in order to help you. diff --git a/docs/index.rst b/docs/index.rst index 4edcef5f..f2d6d087 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -36,7 +36,7 @@ Contents introduction .. toctree:: - :maxdepth: 3 + :maxdepth: 2 :caption: Getting Started installations/installation-on-gnu-linux @@ -45,20 +45,19 @@ Contents .. toctree:: :maxdepth: 2 - :navigation_depth: 4 :caption: Quick Start Guides guides/user-guides/user-quickstart-guide .. toctree:: - :maxdepth: 3 + :maxdepth: 2 :caption: Tutorials tutorials/TOPP/TOPP-tutorial tutorials/TOPPAS/TOPPAS-tutorial .. toctree:: - :maxdepth: 3 + :maxdepth: 2 :caption: OpenMS TOPP Tools topp/topp.md diff --git a/docs/introduction.md b/docs/introduction.md index 34fe90dd..729ad0d5 100644 --- a/docs/introduction.md +++ b/docs/introduction.md @@ -7,14 +7,14 @@ analyses. It offers an infrastructure for rapid development of mass spectrometry related software. OpenMS is free software available under the three clause BSD license and runs under Windows, macOS, and Linux. -It comes with a vast variety of pre-built and ready-to-use tools for proteomics +OpenMS has a vast variety of pre-built and ready-to-use tools for proteomics and metabolomics data analysis (TOPPTools) as well as powerful 1D, 2D and 3D visualization (TOPPView). OpenMS offers analyses for various quantitation protocols, including label-free quantitation, SILAC, iTRAQ, TMT, SRM, SWATH, etc. -It provides built-in algorithms for de-novo identification and database search, +OpenMS 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, Mascot, OMSSA, etc. It supports easy integration of OpenMS built tools into workflow engines like KNIME, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and diff --git a/docs/topp/ini-file-editor.md b/docs/topp/ini-file-editor.md index e5635936..6012e92c 100644 --- a/docs/topp/ini-file-editor.md +++ b/docs/topp/ini-file-editor.md @@ -7,4 +7,4 @@ The values can be edited by double-clicking or pressing F2. The documentation of each value is shown in the text area on the bottom of the widget. -![](../../images/topp/INIFileEditor.png) +![INIFileEditor](../images/topp/INIFileEditor.png) diff --git a/docs/topp/swathwizard.md b/docs/topp/swathwizard.md index 0b26a647..22412fdd 100644 --- a/docs/topp/swathwizard.md +++ b/docs/topp/swathwizard.md @@ -16,9 +16,9 @@ both the intermediate files from OpenSWATH (e.g. the XIC data in `.sqMass` forma This is how the wizard looks like: -![](../../images/topp/SwathWizard.png) +![SwathWizard](../images/topp/SwathWizard.png) -Schematic of the internal data flow (all tools are called by SwathWizard in the background) can be found in the +A schematic of the internal data flow (all tools are called by SwathWizard in the background) can be found in the [TOPP Documentation: SwathWizard](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_SwathWizard.html). A recommended test data for the Wizard is the [PASS00779](https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_View?identifier=PASS00779) dataset. diff --git a/docs/topp/toppas.md b/docs/topp/toppas.md index 6a7f777e..cd2e7e7c 100644 --- a/docs/topp/toppas.md +++ b/docs/topp/toppas.md @@ -11,11 +11,11 @@ up and saved, a workflow can also be run without the GUI using the `ExecutePipel The following figure shows a simple example pipeline that has just been created and executed successfully: -![](../../images/topp/TOPPAS_simple_example.png) +![TOPPAS simple example](../images/topp/TOPPAS_simple_example.png) -More information about TOPPAS can be found in the [TOPPAS tutorial](../../tutorials/TOPP/TOPPAS-tutorial.md). +More information about TOPPAS can be found in the [TOPPAS tutorial](../tutorials/TOPP/TOPPAS-tutorial.md). -The command line parameters of this tool are: +**The command line parameters of this tool are**: ``` TOPPAS -- An assistant for GUI-driven TOPP workflow design. diff --git a/docs/topp/toppview.md b/docs/topp/toppview.md index abcd5bba..ecf1cf6f 100644 --- a/docs/topp/toppview.md +++ b/docs/topp/toppview.md @@ -5,9 +5,9 @@ TOPPView file formats. It also supports viewing data from an OpenMS database. The following figure shows two instances of TOPPView displaying a HPLC-MS map and a MS raw spectrum: -![](../../images/topp/TOPPView.png) +![TOPPView](../images/topp/TOPPView.png) -More information about TOPPView can be found in the [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md). +More information about TOPPView can be found in the [TOPP tutorial](../tutorials/TOPP/TOPP-tutorial.md). **The command line parameters of this tool are**: diff --git a/docs/tutorials/TOPP/consensus-peptide-identification.md b/docs/tutorials/TOPP/consensus-peptide-identification.md index bd132405..74658911 100644 --- a/docs/tutorials/TOPP/consensus-peptide-identification.md +++ b/docs/tutorials/TOPP/consensus-peptide-identification.md @@ -11,11 +11,12 @@ In order to improve the identification accuracy, several identification engines identification can be calculated from the results. The image below shows an example where Mascot and OMSSA results are fed to the **ConsensusID** tool (ConsensusID is currently usable for Mascot, OMSSA and XTandem). -![](../../images/tutorials/topp/TOPP_consensus_id.png) +![TOPP Consensus ID](../../images/tutorials/topp/TOPP_consensus_id.png) To combine quantitation and identification results: Protein/peptide identifications can be annotated to quantitation results (featureXML, consensusXML) by the **IDMapper** tool. The combined results can then be exported by the **TextExporter** tool: + [Conversion between OpenMS XML formats and text formats](conversion-between-openms-xml-formats-and-text-formats.md). diff --git a/docs/tutorials/TOPP/data-analysis-in-toppview.md b/docs/tutorials/TOPP/data-analysis-in-toppview.md index 4b30b5e8..b6beb86d 100644 --- a/docs/tutorials/TOPP/data-analysis-in-toppview.md +++ b/docs/tutorials/TOPP/data-analysis-in-toppview.md @@ -4,14 +4,14 @@ Data Analysis in TOPPView TOPPView also offers limited data analysis capabilities for single layers, which will be illustrated in the following sections. The functionality presented here can be found in the **Tools** menu: -![](../../images/tutorials/topp/TOPPView_tools_menu.png) +![TOPPView Tools Menu](../../images/tutorials/topp/TOPPView_tools_menu.png) ## TOPP Tools Single TOPP tools can be applied to the data of the currently selected layer or to the visible data of the current layer. The following example image shows the TOPP tools dialog: -![](../../images/tutorials/topp/TOPPView_tools.png) +![TOPPView Tools](../../images/tutorials/topp/TOPPView_tools.png) To apply a TOPP tool, follow the instructions below: @@ -25,7 +25,7 @@ To apply a TOPP tool, follow the instructions below: One can access the metadata, the layer is annotated with. This data comprises e.g. contact person, instrument description and sample description. -![](../../images/tutorials/topp/MetaDataBrowser.png) +![Meta Data Browser](../../images/tutorials/topp/MetaDataBrowser.png) > **_NOTE:_** Identification data, e.g. from a Mascot run, can be annotated to the spectra or features, too. After annotation, this data is listed in the metadata. @@ -35,4 +35,4 @@ annotation, this data is listed in the metadata. Statistics about peak/feature intensities and peak meta information can be displayed. For intensities, it is possible to display an additional histogram view. -![](../../images/tutorials/topp/TOPPView_statistics.png) +![TOPPView Statistics](../../images/tutorials/topp/TOPPView_statistics.png) diff --git a/docs/tutorials/TOPP/display-modes-and-view-options.md b/docs/tutorials/TOPP/display-modes-and-view-options.md index 5a862eea..503d3c41 100644 --- a/docs/tutorials/TOPP/display-modes-and-view-options.md +++ b/docs/tutorials/TOPP/display-modes-and-view-options.md @@ -4,7 +4,7 @@ Display Modes and View Options in TOPPView All of the views support several display modes and view options. Display modes determine how intensities are displayed. View options configure the view. -![](../../images/tutorials/topp/TOPPView_icons.png) +![TOPPView Icons](../../images/tutorials/topp/TOPPView_icons.png) # Display Modes diff --git a/docs/tutorials/TOPP/feature-detection-on-centroided-data.md b/docs/tutorials/TOPP/feature-detection-on-centroided-data.md index 9ffc0347..b837bd6c 100644 --- a/docs/tutorials/TOPP/feature-detection-on-centroided-data.md +++ b/docs/tutorials/TOPP/feature-detection-on-centroided-data.md @@ -28,4 +28,4 @@ traces, a tolerated mass deviation between isotopic peaks has to be set (`isotop The image shows the centroided peak data and the found peptide features. The used parameters can be found in the TOPP tools dialog. -![](../../images/tutorials/topp/TOPPView_tools_ff_centroided.png) +![TOPPView Tools FF\_Centrioided](../../images/tutorials/topp/TOPPView_tools_ff_centroided.png) diff --git a/docs/tutorials/TOPP/feature-grouping.md b/docs/tutorials/TOPP/feature-grouping.md index 678d734c..171ce16c 100644 --- a/docs/tutorials/TOPP/feature-grouping.md +++ b/docs/tutorials/TOPP/feature-grouping.md @@ -21,13 +21,13 @@ To differentially quantify the features of an isotope-labeled HPLC-MS map, follo - feature quality of feature 2 - quality measure for the shift (how near is it to the optimal shift) - ![](../../images/tutorials/topp/TOPP_labeled_quant.png) + ![TOPP labeled quant](../../images/tutorials/topp/TOPP_labeled_quant.png) ## Label-free quantitation To differentially quantify the features of two or more label-free HPLC-MS map. -![](../../images/tutorials/topp/TOPP_labelfree_quant.png) +![TOPP labelfree quant](../../images/tutorials/topp/TOPP_labelfree_quant.png) > **_NOTE:_** This algorithm assumes that the retention time axes of all input maps are very similar. To correct for retention time distortions, please have a look at [Map alignment](map-alignment.md). diff --git a/docs/tutorials/TOPP/general-introduction.md b/docs/tutorials/TOPP/general-introduction.md index a7521110..0724f8c1 100644 --- a/docs/tutorials/TOPP/general-introduction.md +++ b/docs/tutorials/TOPP/general-introduction.md @@ -73,7 +73,7 @@ command line flag `-help`. Some TOPP tools also have subsections of parameters t algorithm. The documentation of these subsections is not displayed with `–help`. It is however displayed in **INIFileEditor**. -![](../../images/tutorials/topp/INIFileEditor.png) +![INIFileEditor](../../images/tutorials/topp/INIFileEditor.png) In the [INIFileEditor](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_INIFileEditor.html), click on the respective parameter, the documentation of the parameters is displayed in the window at the bottom. diff --git a/docs/tutorials/TOPP/map-alignment.md b/docs/tutorials/TOPP/map-alignment.md index f1a23e59..c88dc781 100644 --- a/docs/tutorials/TOPP/map-alignment.md +++ b/docs/tutorials/TOPP/map-alignment.md @@ -9,7 +9,7 @@ corrects for shifted and scaled retention times, which may result from changes o The different **MapAligner** tools take `n` input maps, de-warp them and store the `n` de-warped maps. The following image shows the general procedure: -![](../../images/tutorials/topp/TOPP_alignment.png) +![TOPP Alignment](../../images/tutorials/topp/TOPP_alignment.png) There are different map alignment tools available. The following table gives a rough overview of them: diff --git a/docs/tutorials/TOPP/picking-peaks.md b/docs/tutorials/TOPP/picking-peaks.md index 3aaae8eb..2b397e47 100644 --- a/docs/tutorials/TOPP/picking-peaks.md +++ b/docs/tutorials/TOPP/picking-peaks.md @@ -23,4 +23,4 @@ good values, consider changing the advanced parameter `fwhm_lower_bound_factor` The following image shows a part of the spectrum with the picked peaks shown in green, the estimated peak width in the log window and the measured peak width. -![](../../images/tutorials/topp/TOPPView_tools_pp_picked.png) +![TOPPView tools pp\_picked](../../images/tutorials/topp/TOPPView_tools_pp_picked.png) diff --git a/docs/tutorials/TOPP/profile-data-processing.md b/docs/tutorials/TOPP/profile-data-processing.md index 5d47780f..55340593 100644 --- a/docs/tutorials/TOPP/profile-data-processing.md +++ b/docs/tutorials/TOPP/profile-data-processing.md @@ -9,7 +9,7 @@ To find all peaks in the profile data: 2. The now smoothed profile data can be further processed by subtracting the baseline with the **BaselineFilter**. 3. Then use one of the **PeakPickers** to find all peaks in the baseline-reduced profile data. -![](../../images/tutorials/topp/TOPP_raw_data.png) +![TOPP raw data](../../images/tutorials/topp/TOPP_raw_data.png) There are two different smoothing filters: NoiseFilterGaussian and NoiseFilterSGolay. To use the Savitzky Golay filter, or the **BaselineFilter** with non equally spaced profile data, e.g. TOF data, you have to generate equally spaced data @@ -62,4 +62,4 @@ good parameters, following this procedure: 2. Extract a single scan from the middle of the HPLC gradient (Right click on **scan**). 3. Experiment with the parameters until you have found the proper settings -You can find the **NoiseFilters**, the **BaselineFilter**, and the **PeakPickers** in **TOPPView** in the menu **Layer** > **Apply TOPP tool**. +Find the **NoiseFilters**, the **BaselineFilter**, and the **PeakPickers** in **TOPPView** in the menu **Layer** > **Apply TOPP tool**. diff --git a/docs/tutorials/TOPP/quality-control.md b/docs/tutorials/TOPP/quality-control.md index d4fca253..ce539273 100644 --- a/docs/tutorials/TOPP/quality-control.md +++ b/docs/tutorials/TOPP/quality-control.md @@ -12,7 +12,7 @@ then be processed using custom scripts or via the R package (see [github:cbielow ![](../../images/tutorials/topp/TOPP_qualitycontrol.png) -An example workflow can be found in `OpenMS/share/OpenMS/examples/TOPPAS/QualityControl.toppas`. +Find an example workflow in `OpenMS/share/OpenMS/examples/TOPPAS/QualityControl.toppas`. For data from [TOPP Documentation:IsobaricAnalyzer](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IsobaricAnalyzer.html), just provide the consensusXML as input to [TOPP Documentation:QualityControl](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_QualityControl.html). No FeatureXMLs or TrafoXMLs are required. The mzML raw file can be added as input though. diff --git a/docs/tutorials/TOPP/subtracting-a-baseline-from-a-spectrum.md b/docs/tutorials/TOPP/subtracting-a-baseline-from-a-spectrum.md index f329e8e7..10932ef2 100644 --- a/docs/tutorials/TOPP/subtracting-a-baseline-from-a-spectrum.md +++ b/docs/tutorials/TOPP/subtracting-a-baseline-from-a-spectrum.md @@ -8,9 +8,10 @@ between different types of filters (green rectangle), the one mainly used is Top the length of the structuring element (blue rectangle). The default value is `3` Thomson. Press **Ok** to start the baseline subtraction. -![](../../images/tutorials/topp/TOPPView_tools_baseline.png) +![TOPPView Tools Baseline](../../images/tutorials/topp/TOPPView_tools_baseline.png) -The following image shows a part of the spectrum after baseline filtering as green line, the original raw data is shown -by the blue line. +The following image shows: +- A part of the spectrum after baseline filtering as a green line +- The original raw data as a blue line. -![](../../images/tutorials/topp/TOPPView_tools_baseline_filtered.png) +![TOPPView Tools Baseline Filtered](../../images/tutorials/topp/TOPPView_tools_baseline_filtered.png) diff --git a/docs/tutorials/TOPP/toppview-introduction.md b/docs/tutorials/TOPP/toppview-introduction.md index 000c7b24..961f2132 100644 --- a/docs/tutorials/TOPP/toppview-introduction.md +++ b/docs/tutorials/TOPP/toppview-introduction.md @@ -10,4 +10,4 @@ datasets as well as displaying input data and output data of an algorithm togeth TOPPView is intended for visual inspection of the data by experimentalists as well as for analysis software by developers. -![](../../images/tutorials/topp/TOPPView_parts.png) +![TOPPView Parts](../../images/tutorials/topp/TOPPView_parts.png) diff --git a/docs/tutorials/TOPP/views-in-toppview.md b/docs/tutorials/TOPP/views-in-toppview.md index 585624fd..63b9eb98 100644 --- a/docs/tutorials/TOPP/views-in-toppview.md +++ b/docs/tutorials/TOPP/views-in-toppview.md @@ -51,7 +51,7 @@ annotations and text labels have been added by right-clicking peaks and selectin clicking anywhere and selecting **Add Label**, respectively. Multiple annotations can be selected by holding down the `CTRL` key while clicking them. They can be moved around by dragging the mouse and deleted by pressing `DEL`. -![](../../images/tutorials/topp/TOPPView_1D.png) +![TOPPView 1D](../../images/tutorials/topp/TOPPView_1D.png) Through the **context menu**: of the 1D view you can: @@ -70,7 +70,7 @@ layer individually. The following example image shows a small section of a peak map and the detected features in a second layer. -![](../../images/tutorials/topp/Plot2DWidget.png) +![Plot 2D Widget](../../images/tutorials/topp/Plot2DWidget.png) In addition to the normal top-down view, the 2D view can display the projections of the data to the `m/z` and `RT` axis. This feature is mainly used to assess the quality of a feature without opening the data region in 3D view. @@ -93,7 +93,7 @@ layer individually. The following example image shows a small region of a peak map: -![](../../images/tutorials/topp/Plot3DWidget.png) +![Plot 3D Widget](../../images/tutorials/topp/Plot3DWidget.png) Through the **context menu**: of the 3D view you can: diff --git a/docs/tutorials/TOPPAS/examples.md b/docs/tutorials/TOPPAS/examples.md index 74fd1afd..127768cd 100644 --- a/docs/tutorials/TOPPAS/examples.md +++ b/docs/tutorials/TOPPAS/examples.md @@ -13,7 +13,7 @@ noise-filtered and baseline-reduced profile data. This workflow is also describe [Profile data processing](../TOPP/profile-data-processing.md). The individual steps are explained in more detail in the TOPPView tutorial: [Smoothing raw data](../TOPP/smoothing-raw-data.md), [Subtracting a baseline from a spectrum](../TOPP/subtracting-a-baseline-from-a-spectrum.md), and [Picking peaks](../TOPP/picking-peaks.md). -![](../../images/tutorials/toppas/TOPPAS_example_profile_data_processing.png) +![TOPPAS Example Profile Data Processing](../../images/tutorials/toppas/TOPPAS_example_profile_data_processing.png) ## Identification of E. coli peptides @@ -32,7 +32,7 @@ path to the OMSSA executable (omssacl) must be set in the parameters of the OMSS - FalseDiscoveryRate computes q-values for the IDs. - Finally, IDFilter selects only those IDs with a q-value of less than 1%. -![](../../images/tutorials/toppas/TOPPAS_Ecoli_Identification.png) +![TOPPAS Ecoli Identification](../../images/tutorials/toppas/TOPPAS_Ecoli_Identification.png) Extensions to this pipeline would be to do the annotation of the spectra with multiple search engines and combine the results afterwards, using the **ConsensusID** TOPP tool. @@ -44,28 +44,30 @@ The results may be exported using the **TextExporter** tool, for further analysi The simple pipeline described in this section (`BSA_Quantitation.toppas`) can be used to quantify peptides that occur on different runs. The example dataset contains three different bovine serum albumin (BSA) runs. First, **FeatureFinderCentroided** is called since the dataset is centroided. The results of the feature finding are then annotated with (existing) identification results. For convenience, we provide these search results from OMSSA with peptides with an FDR of 5% in the BSA directory. -![](../../images/tutorials/toppas/TOPPAS_BSA_Quantitation.png) +![TOPPAS BSA Quantitation](../../images/tutorials/toppas/TOPPAS_BSA_Quantitation.png) Identifications are mapped to features by the **IDMapper**. The last step is performed by **FeatureLinkerUnlabeled** which links corresponding features. The results can be used to calculate ratios, for example. The data could also be exported to a text based format using the TextExporter for further processing (e.g., in Microsoft Excel). The results can be opened in TOPPView. The next figures show the results in 2D and 3D view, together with the feature -intermediate results. One can see that the intensities and retention times are slightly different between the runs. To -correct for retention times shift, a map alignment could be done, either on the spectral data or on the feature data. +intermediate results. -![](../../images/tutorials/toppas/TOPPAS_BSA_results_2d.png) +> **_NOTE:_** The intensities and retention times are slightly different between the runs. To correct for retention +times shift, a map alignment could be done, either on the spectral data or on the feature data. -![](../../images/tutorials/toppas/TOPPAS_BSA_results_3d.png) +![TOPPAS BSA Results 2D](../../images/tutorials/toppas/TOPPAS_BSA_results_2d.png) + +![TOPPAS BSA Results 3D](../../images/tutorials/toppas/TOPPAS_BSA_results_3d.png) ## Merger and Collect nodes -The following example is actually not a useful workflow but is supposed to demonstrate how merger and collector nodes -can be used in a pipeline. Have a look at `merger_tutorial.toppas`: +The following example is trivial but demonstrates how merger and collector nodes can be used in a pipeline. Have a look +at `merger_tutorial.toppas`: -![](../../images/tutorials/toppas/TOPPAS_example_merger.png) +![TOPPAS Example Merger](../../images/tutorials/toppas/TOPPAS_example_merger.png) -As its name suggests, a merger merges its incoming file lists, i.e., files of all incoming edges are appended into new +A Merger merges its incoming file lists, i.e., files of all incoming edges are appended into new lists (which have as many elements as the merger has incoming connections). All tools this merger has outgoing connections to are called with these merged lists as input files. All incoming connections should pass the same number of files (unless the corresponding preceding tool is in recycling mode). diff --git a/docs/tutorials/TOPPAS/general-introduction.md b/docs/tutorials/TOPPAS/general-introduction.md index 20d4bbad..5a0b44d2 100644 --- a/docs/tutorials/TOPPAS/general-introduction.md +++ b/docs/tutorials/TOPPAS/general-introduction.md @@ -9,7 +9,7 @@ invalid workflows. Once set up and saved, a workflow can also be run without the The following figure shows a simple example pipeline that has just been created and executed successfully: -![](../../images/tutorials/toppas/TOPPAS_simple_example.png) +![TOPPAS Simple Example](../../images/tutorials/toppas/TOPPAS_simple_example.png) To create a new TOPPAS file, do any of the following: diff --git a/docs/tutorials/TOPPAS/user-interface.md b/docs/tutorials/TOPPAS/user-interface.md index a5420377..c96d55ed 100644 --- a/docs/tutorials/TOPPAS/user-interface.md +++ b/docs/tutorials/TOPPAS/user-interface.md @@ -19,7 +19,7 @@ workflow, or if it just would not make sense, e.g. if its target is an input fil file node (#1) and the OMSSAAdapter (#5) tool is painted yellow which indicates it is not ready yet, because no input files have been specified. -![](../../images/tutorials/TOPPAS_edges.png) +![TOPPAS Edges](../../images/tutorials/TOPPAS_edges.png) The input/output mapping of connections can be changed at any time during the editing process by double-clicking an connections or by selecting **Edit I/O mapping** from the context menu which appears when a connection is right-clicked. @@ -30,24 +30,24 @@ The following figure shows a possible next step: the user has double-clicked one its parameters. By default, the standard parameters are used for each tool. Again, this can also be done by selecting **Edit parameters** from the context menu of the tool. -![](../../images/tutorials/TOPPAS_parameters.png) +![TOPPAS Parameters](../../images/tutorials/TOPPAS_parameters.png) -Once the pipeline has been set up, the input files have to be specified before the pipeline can be executed. This is -done by double-clicking an input node and selecting the desired files in the dialog that appears. Input nodes have a -special mode named **recycling mode**, i.e., if the input node has fewer files than the following node has rounds -(as it might have two incoming connections) then the files are recycled until all rounds are satisfied. This might be -useful if one input node specifies a single database file (for a Search-Adapter like Mascot) and another input node has -the actual MS2 experiments (which is usually more than one). Then the database input node would be set to `recycle` the -database file, i.e. use it for every run of the MascotAdapter node. The input list can be recycled an arbitrary number -of times, but the recycling has to be `complete`, i.e. the number of rounds of the downstream node have to be a multiple -of the number of input files. Recycling mode can be activated by right-clicking the input node and selecting the according -entry from the context menu. Finally, if you have input and output nodes at every end of your pipeline and all -connections are green, select **Pipeline** > **Run** in the menu bar or just press `F5`. +Once the pipeline has been set up, specify the input files before executing the pipeline. This is done by double-clicking +an input node and selecting the desired files in the dialog that appears. Input nodes have a special mode named +**recycling mode**, i.e., if the input node has fewer files than the following node has rounds (as it might have two +incoming connections) then the files are recycled until all rounds are satisfied. This might be useful if one input node +specifies a single database file (for a Search-Adapter like Mascot) and another input node has the actual MS2 experiments +(which is usually more than one). Then the database input node would be set to `recycle` the database file, i.e. use it for +every run of the MascotAdapter node. The input list can be recycled an arbitrary number of times, but the recycling has to be +`complete`, i.e. the number of rounds of the downstream node have to be a multiple of the number of input files. Recycling mode +can be activated by right-clicking the input node and selecting the according entry from the context menu. Finally, if you have +input and output nodes at every end of your pipeline and all connections are green, select **Pipeline** > **Run** in the menu +bar or just press `F5`. -![](../../images/tutorials/TOPPAS_run_options.png) +![TOPPAS Run Options](../../images/tutorials/TOPPAS_run_options.png) -When asked for an output file directory where a sub-directory, `TOPPAS_out`, will be created. This directory will -contain the output files. Specify the number of jobs TOPPAS is allowed to run in parallel, if a number greater than 1 is +When asked for an output file directory `TOPPAS_out` as sub-directory, will be created. This directory will +contain the output files. Specify the number of jobs TOPPAS is allowed to run in parallel. If a number greater than 1 is selected, TOPPAS will parallelize the pipeline execution in the following scenarios: - A tool has to process more than one file. In this case, multiple files can be processed in parallel. From 0ec8d9fadf74671df9d71400e05dd3daebcaa33b Mon Sep 17 00:00:00 2001 From: Tapasweni Pathak Date: Wed, 25 May 2022 09:35:24 +0530 Subject: [PATCH 2/2] review fixes and add a few links to tutorials --- docs/contact-us.md | 3 +-- docs/guides/user-guides/user-quickstart-guide.md | 8 ++++---- .../TOPP/subtracting-a-baseline-from-a-spectrum.md | 2 +- 3 files changed, 6 insertions(+), 7 deletions(-) diff --git a/docs/contact-us.md b/docs/contact-us.md index b78a4079..b46e0625 100644 --- a/docs/contact-us.md +++ b/docs/contact-us.md @@ -7,8 +7,7 @@ Contact us: 2. Drop us an email at user support [open-ms-general](https://sourceforge.net/projects/open-ms/lists/open-ms-general) mailing list. 3. To stay updated of new versions of OpenMS and releases, subscribe to [openms-announcements mailing list](https://sourceforge.net/projects/open-ms/lists/open-ms-announcements). -4. In order to report a new bug, please create an issue on GitHub [OpenMS](https://github.com/OpenMS/OpenMS/issues) - repository. +4. To report a new bug, create an issue on GitHub [OpenMS](https://github.com/OpenMS/OpenMS/issues) repository. Say hi on [OpenMS Twitter](https://twitter.com/openmsteam)! diff --git a/docs/guides/user-guides/user-quickstart-guide.md b/docs/guides/user-guides/user-quickstart-guide.md index 8bd0ea8a..4ca93ea3 100644 --- a/docs/guides/user-guides/user-quickstart-guide.md +++ b/docs/guides/user-guides/user-quickstart-guide.md @@ -19,19 +19,19 @@ Before using OpenMS, become familiar with the following terms: |--------------------|-------------| |**TOPPView** |A design tool that is used to view and explore LC-MS data, alignments, groups, peptide identifications, and more.| |**TOPPAS** |A graphical workflow design tool that is used to create pipelines from all TOPP tools (and 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 TOPP tools are accessible from a command prompt/shell or via TOPPAS. See also: [TOPP tutorial]() and [TOPP documentation](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_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 TOPP tools are accessible from a command prompt/shell or via TOPPAS. See also: [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md) and [TOPP documentation](../../topp/topp.md)| |**UTILS** |Similar to 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)| ## How to run a Tool A good start are the example pipelines (select **File** > **Open example file** within TOPPAS). -Read the documentation of the tools (see [TOPP tutorial](), [TOPP documentation](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_documentation.html)) and the one of TOPPAS ([TOPPAS tutorial](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_documentation.html)). +Read the documentation of the tools (see [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md), [TOPP documentation](../../topp/topp.md) and the one of TOPPAS ([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. -## Adapting your pipeline parameters +## Adapte pipeline parameters The default parameters of each tool can usually be tweaked to fit the data and improve results. @@ -48,7 +48,7 @@ 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](), which is another GUI tool shipped with + 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 OpenMS and similar to the one build into TOPPAS. ### How do I feed the INI file to a Tool? diff --git a/docs/tutorials/TOPP/subtracting-a-baseline-from-a-spectrum.md b/docs/tutorials/TOPP/subtracting-a-baseline-from-a-spectrum.md index 10932ef2..ff7227ef 100644 --- a/docs/tutorials/TOPP/subtracting-a-baseline-from-a-spectrum.md +++ b/docs/tutorials/TOPP/subtracting-a-baseline-from-a-spectrum.md @@ -11,7 +11,7 @@ subtraction. ![TOPPView Tools Baseline](../../images/tutorials/topp/TOPPView_tools_baseline.png) The following image shows: -- A part of the spectrum after baseline filtering as a green line +- A part of the spectrum after baseline filtering as a green line. - The original raw data as a blue line. ![TOPPView Tools Baseline Filtered](../../images/tutorials/topp/TOPPView_tools_baseline_filtered.png)