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* Add sections.py * Add quant_proteomics.py * Add data.py * Add post_processing_visualisation.py --------- Co-authored-by: Cameron Hyde <[email protected]>
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| from . import ( | ||
| data, | ||
| post_processing_visualisation, | ||
| quant_proteomics, | ||
| ) |
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| """Content for data section - tools, workflows and help tabs.""" | ||
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| galaxy_au_support_item = { | ||
| "title_html": 'Galaxy Australia support', | ||
| "description_html": """<p> | ||
| Any user of Galaxy Australia can request support through an | ||
| online form. | ||
| </p>""", | ||
| "button_link": "/request/support", | ||
| "button_html": "Request support", | ||
| } | ||
|
|
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| tools = [ | ||
| # { # Accordion item schema: | ||
| # "title_html": '', | ||
| # "description_html": """""", | ||
| # "inputs": [ | ||
| # { | ||
| # 'datatypes': [''], | ||
| # 'label': '', | ||
| # }, | ||
| # ], | ||
| # "button_link": "", | ||
| # "button_html": "", | ||
| # "button_tip": "", | ||
| # "view_link": "", | ||
| # "view_html": "", | ||
| # "view_tip": "", | ||
| # }, | ||
| { | ||
| "title_html": "Import data to Galaxy", | ||
| "description_html": "<p>Standard upload of data to Galaxy, from your computer or from the web.</p>", | ||
| "button_link": 'https://genome.usegalaxy.org.au/tool_runner?tool_id=upload1', | ||
| } | ||
| ] | ||
|
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|
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| help = [ | ||
| { | ||
| "title_html": 'Can I upload sensitive data?', | ||
| "description_html": """ | ||
| <p> | ||
| No, do not upload personal or sensitive, such as human health or clinical data. | ||
| Please see our | ||
| <a href="/about#data-privacy">Data Privacy</a> | ||
| page for definitions of sensitive and health-related information. | ||
| </p> | ||
| <p> | ||
| Please also make sure you have read our | ||
| <a href="/about#terms-of-service">Terms of Service</a>, | ||
| which covers hosting and analysis of research data. | ||
| </p>""", | ||
| }, | ||
| { | ||
| "title_html": 'Is my data private?', | ||
| "description_html": """ | ||
| <p> | ||
| Please read our | ||
| <a href="/about#data-privacy">Privacy Policy</a> | ||
| for information on your personal data and any data that you upload. | ||
| </p>""", | ||
| }, | ||
| { | ||
| "title_html": 'How can I increase my storage quota?', | ||
| "description_html": """ | ||
| <p> | ||
| Please submit a quota request if your Galaxy Australia account reaches its data storage limit. Requests are usually provisioned quickly if you provide a reasonable use case for your request. | ||
| </p>""", | ||
| "button_link": "/request/quota", | ||
| "button_html": "Request", | ||
| }, | ||
| { | ||
| "title_html": 'Tutorial: Introduction to proteomics, protein identification, quantification and statistical modelling', | ||
| "description_html": """ | ||
| <p> | ||
| This practical aims to familiarize you with Galaxy for Proteomics, including theory, methods and software examples. | ||
| </p>""", | ||
| "button_link": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/introduction/slides.html#1", | ||
| "button_html": "Tutorial", | ||
| }, | ||
| galaxy_au_support_item, | ||
| ] |
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webapp/home/subdomains/proteomics/content/post_processing_visualisation.py
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| """Content for data section - tools, workflows and help tabs.""" | ||
|
|
||
| galaxy_au_support_item = { | ||
| "title_html": 'Galaxy Australia support', | ||
| "description_html": """<p> | ||
| Any user of Galaxy Australia can request support through an | ||
| online form. | ||
| </p>""", | ||
| "button_link": "/request/support", | ||
| "button_html": "Request support", | ||
| } | ||
|
|
||
| tools = [ | ||
| # { # Accordion item schema: | ||
| # "title_html": '', | ||
| # "description_html": """""", | ||
| # "inputs": [ | ||
| # { | ||
| # 'datatypes': [''], | ||
| # 'label': '', | ||
| # }, | ||
| # ], | ||
| # "button_link": "", | ||
| # "button_html": "", | ||
| # "button_tip": "", | ||
| # "view_link": "", | ||
| # "view_html": "", | ||
| # "view_tip": "", | ||
| # }, | ||
| { | ||
| "title_html": '<code>LFQ Analyst</code>', | ||
| "description_html": '<p>Analyze and Visualize Label-Free Proteomics output from MaxQuant.</p>', | ||
| "inputs": [ | ||
| { | ||
| 'datatypes': ['txt'], | ||
| 'label': 'Protein groups (MaxQuant output)', | ||
| }, | ||
| { | ||
| 'datatypes': ['txt'], | ||
| 'label': 'Experimental Design Matrix (MaxQuant output)', | ||
| } | ||
| ], | ||
| "button_link": "https://usegalaxy.org.au/root?tool_id=interactive_tool_lfqanalyst", | ||
| "view_link": "Shah AD, Goode RJA, Huang C, Powell DR, Schittenhelm RB. LFQ-Analyst: An easy-to-use interactive web-platform to analyze and visualize proteomics data preprocessed with MaxQuant. https://doi.org/10.1021/acs.jproteome.9b00496", | ||
| }, | ||
| { | ||
| "title_html": '<code>MSstats</code>', | ||
| "description_html": '<p>Statistical relative protein significance analysis in DDA, SRM and DIA Mass Spectrometry.</p>', | ||
| "inputs": [ | ||
| { | ||
| 'datatypes': ['tabular', 'csv'], | ||
| 'label': 'Either the 10-column MSstats format or the outputs of spectral processing tools such as MaxQuant, OpenSWATH.', | ||
| } | ||
| ], | ||
| "button_link": "https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/", | ||
| } | ||
| ] | ||
|
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| help = [ | ||
| { | ||
| "title_html": 'LFQ-Analyst: Manual', | ||
| "description_html": """ | ||
| <p> | ||
| A detailed user manual for LFQ-Analyst. | ||
| </p>""", | ||
| "button_link": "https://analyst-suite.monash-proteomics.cloud.edu.au/apps/lfq-analyst/LFQ-Analyst_manual.pdf", | ||
| "button_html": "Manual", | ||
| "view_link": "Shah AD, Goode RJA, Huang C, Powell DR, Schittenhelm RB. LFQ-Analyst: An easy-to-use interactive web-platform to analyze and visualize proteomics data preprocessed with MaxQuant. https://doi.org/10.1021/acs.jproteome.9b00496", | ||
| }, | ||
| { | ||
| "title_html": 'MaxQuant and MSstats for the analysis of label-free data', | ||
| "description_html": """ | ||
| <p> | ||
| Learn how to use MaxQuant and MSstats for the analysis of label-free shotgun (DDA) data. | ||
| </p>""", | ||
| "button_link": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.html", | ||
| "button_html": "Tutorial", | ||
| }, | ||
| galaxy_au_support_item, | ||
| ] |
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57
webapp/home/subdomains/proteomics/content/quant_proteomics.py
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,57 @@ | ||
| """Content for data section - tools, workflows and help tabs.""" | ||
|
|
||
| galaxy_au_support_item = { | ||
| "title_html": 'Galaxy Australia support', | ||
| "description_html": """<p> | ||
| Any user of Galaxy Australia can request support through an | ||
| online form. | ||
| </p>""", | ||
| "button_link": "/request/support", | ||
| "button_html": "Request support", | ||
| } | ||
|
|
||
| tools = [ | ||
| # { # Accordion item schema: | ||
| # "title_html": '', | ||
| # "description_html": """""", | ||
| # "inputs": [ | ||
| # { | ||
| # 'datatypes': [''], | ||
| # 'label': '', | ||
| # }, | ||
| # ], | ||
| # "button_link": "", | ||
| # "button_html": "", | ||
| # "button_tip": "", | ||
| # "view_link": "", | ||
| # "view_html": "", | ||
| # "view_tip": "", | ||
| # }, | ||
| { | ||
| "title_html": '<code>MaxQuant</code>', | ||
| "description_html": '<p>MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.</p>', | ||
| "inputs": [ | ||
| {'datatypes': ['thermo.raw']}, | ||
| {'datatypes': ['mzML']}, | ||
| {'datatypes': ['mzXML']}, | ||
| { | ||
| 'datatypes': ['tabular'], | ||
| 'label': 'Experimental design template', | ||
| }, | ||
| ], | ||
| "button_link": "https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/", | ||
| }, | ||
| { | ||
| "title_html": '<code>FlashLFQ</code>', | ||
| "description_html": '<p>Ultrafast label-free quantification for mass-spectrometry proteomics.</p>', | ||
| "inputs": [ | ||
| { | ||
| 'datatypes': ['tabular'], | ||
| 'label': 'MetaMorpheus, Morpheus, PeptideShaker PSM Report, MaxQuant', | ||
| } | ||
| ], | ||
| "button_link": "https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/flashlfq/flashlfq/", | ||
| } | ||
| ] | ||
|
|
||
| help = [] # Todo |
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