modif

.github/workflows/publish.yml

@@ -37,7 +37,7 @@ jobs:
         uses: quarto-dev/quarto-actions/setup@v2
 
       - name: Install GDAL, UDUNITS2
-        run: sudo apt install libgdal-dev libudunits2-dev
+        run: sudo apt update; sudo apt install libgdal-dev libudunits2-dev
 
       - name: Install R
         uses: r-lib/actions/setup-r@v2

.gitignore

@@ -1,8 +1,7 @@
-.swp
 .*.swp
 .Rproj.user
 .Rhistory
 /.quarto/*
 ./docs/*
-/.quarto/
-docs/*
+docs/*
+_freeze/*

W4M_datasets/GCMSIdealg.qmd

@@ -1,23 +1,31 @@
 ---
-title: "GC-MS Idealg dataset"
-doi: "[@DITTAMI_2012](https://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-313X.2012.04982.x)"
-author: "Dittami et al."
-description: "Towards deciphering dynamic changes and evolutionary mechanisms involved in the adaptation to low salinities in Ectocarpus (brown algae)"
-bibliography: "../references.bib"
-galaxyref: "W4M00004"
-W4M: "[history](https://workflow4metabolomics.usegalaxy.fr/published/history?id=85be02a450bd0e8c)"
-link: ""
+  title: "GC-MS Idealg dataset"
+  subtitle: "Towards deciphering dynamic changes and evolutionary mechanisms involved in the adaptation to low salinities in Ectocarpus (brown algae)"
+  doi-link: "[doi link](https://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-313X.2012.04982.x)"
+  author: "Dittami *et al.*, 2012"
+  publication: "@DITTAMI_2012"
+  description: "[doi link](https://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-313X.2012.04982.x)"
+  bibliography: "../references.bib"
+  galaxyref: "W4M00004"
+  W4M: "[W4M00004](https://workflow4metabolomics.usegalaxy.fr/published/history?id=85be02a450bd0e8c)"
+  Respository: ""
 ---
 
+
 ## Description
 
-**Study:** 
+**Background:** Colonizations of freshwater by marine species are rare events, and little information is known about the underlying mechanisms. Brown algae are an independent lineage of photosynthetic and multicellular organisms from which few species inhabit freshwater. As a marine alga that is also found in freshwater, Ectocarpus is of particular interest for studying the transition between these habitats.  
+
+**Objective:** To gain insights into mechanisms of the transition, we examined salinity tolerance and adaptations to low salinities in a freshwater strain of Ectocarpus on physiological and molecular levels.  
+
+**Results:** We show that this isolate belongs to a widely distributed and highly stress-resistant clade, and differed from the genome-sequenced marine strain in its tolerance of low salinities. It also exhibited profound, but reversible, morphological, physiological, and transcriptomic changes when transferred to seawater. Although gene expression profiles were similar in both strains under identical conditions, metabolite and ion profiles differed strongly, the freshwater strain exhibiting e.g. higher cellular contents of amino acids and nitrate, higher contents of n-3 fatty acids, and lower intracellular mannitol and sodium concentrations. Moreover, several stress markers were noted in the freshwater isolate in seawater.  
+
+**Conclusion:** This finding suggests that, while high stress tolerance and plasticity may be prerequisites for the colonization of freshwater, genomic alterations have occurred that produced permanent changes in the metabolite profiles to stabilize the transition.
 
-**Dataset:** 
+**Dataset:**  
 
-**Workflow:** 
+The dataset contains 12 GC-MS injection of *Ectocarpus sp.* (Ectocarpales, Phaeophyceae) samples.
 
-**Comments:** 
+**Workflow:**  
 
-## Citations
-@DITTAMI_2012
+The W4M workflow use XCMS Matched Filter method for peak detection.

W4M_datasets/NMRMusmusculus.qmd

@@ -1,12 +1,14 @@
 ---
 title: "NMR Mus musculus dataset"
-doi: "[publication](https://ehp.niehs.nih.gov/doi/10.1289/ehp.1205588)"
-author: "Cabaton et al."
-description: "Effects of Low Doses of Bisphenol A on the Metabolome of Perinatally Exposed CD-1 Mice"
+subtitle: "Effects of Low Doses of Bisphenol A on the Metabolome of Perinatally Exposed CD-1 Mice"
+doi-link: "[doi link](https://ehp.niehs.nih.gov/doi/10.1289/ehp.1205588)"
+author: "Cabaton *et al.*, 2013"
+publication: "@Cabaton_2013"
+description: "[doi link](https://ehp.niehs.nih.gov/doi/10.1289/ehp.1205588)"
 bibliography: "../references.bib"
 galaxyref: "W4M00006"
-W4M: "[history](https://workflow4metabolomics.usegalaxy.fr/published/history?id=c342a31eb03b9648)"
-link: ""
+W4M: "[W4M00006](https://workflow4metabolomics.usegalaxy.fr/published/history?id=c342a31eb03b9648)"
+Respository: ""
 ---
 
 ## Description
@@ -20,7 +22,3 @@ The dataset contains brain samples from 24 mice pups:
   - Pups sacrificed at 21 days: brain collection  
 
 NMR analysis was performed on a Bruker DRX-600-Avance spectrometer using an inverse detection 5mm cryoprobe attached to a cryoplatform; CPMG spin-echo pulse sequence. Fourier transformation was applied, then all spectra were phased and baseline corrected using TopSpin.
-
-**Workflow:** 
-
-**Comments:** 

W4M_datasets/sacurine.qmd

@@ -1,12 +1,14 @@
 ---
 title: "Sacurine"
-doi: "[publication](https://pubs.acs.org/doi/10.1021/acs.jproteome.5b00354)"
-author: "Thevenot et al."
-description: "Analysis of the human adult urinary metabolome"
+doi-link: "[doi link](https://pubs.acs.org/doi/10.1021/acs.jproteome.5b00354)"
+subtitle: "Analysis of the human adult urinary metabolome"
+publication: "@THEVENOT_2015"
+author: "Thevenot *et al.*, 2015"
+description: "[doi link](https://pubs.acs.org/doi/10.1021/acs.jproteome.5b00354)"
 bibliography: "../references.bib"
 galaxyref: "W4M00001"
-W4M: "[history](https://workflow4metabolomics.usegalaxy.fr/published/history?id=3052e053b71f3ff5)"
-link: "[MTBLS404](https://www.ebi.ac.uk/metabolights/editor/MTBLS404/descriptors)"
+W4M: "[W4M00001](https://workflow4metabolomics.usegalaxy.fr/published/history?id=3052e053b71f3ff5)"
+Respository: "[MTBLS404](https://www.ebi.ac.uk/metabolights/editor/MTBLS404/descriptors)"
 ---
 
 ## Description
@@ -21,4 +23,4 @@ In this study conducted by the MetaboHUB French Infrastructure for Metabolomics,
 This history describes the statistical analysis of the data set from the negative ionization mode (113 identified metabolites at MSI levels 1 or 2): correction of signal drift (loess model built on QC pools) and batch effects (two batches), variable filtering (QC coefficent of variation < 30%), normalization by the sample osmolality, log10 transformation, sample filtering (Hotelling, decile and missing pvalues > 0.001) resulting in the HU_096 sample being discarded, univariate hypothesis testing of significant variations with age, BMI, or between genders (FDR < 0.05), and OPLS(-DA) modeling of age, BMI and gender.
 
 **Comments:** 
-The ‘sacurine’ data set (after normalization and filtering) is also available in the ropls R package from the Bioconductor repository. For a comprehensive analysis of the dataset (starting from the preprocessing of the raw files and including all detected features in the subsequent steps), please see the companion ‘W4M00002_Sacurine-comprehensive’ reference history.
+The ‘sacurine’ data set (after normalization and filtering) is also available in the ropls R package from the Bioconductor repository.

_quarto.yml

@@ -43,6 +43,9 @@ website:
           - text: "Guides for Developpers"
             href: tooldev.qmd
             icon: "code"
+          - text: "Guides for Administrators"
+            href: tooladmin.qmd
+            icon: "code"
           - text: "How to contribute"
             href: contribute.qmd
             icon: "person-fill-up"

renv/.gitignore

@@ -0,0 +1,7 @@
+library/
+local/
+cellar/
+lock/
+python/
+sandbox/
+staging/

tooladmin.qmd

@@ -0,0 +1,45 @@
+---
+  title: "Tool administration"
+---
+
+## How to include the tools supported by W4M in one's Galaxy instance?
+
+As Workflow4Metabolomics, we provide and support a range of tools that are made available at workflow4metabolomics.usegalaxy.fr, 
+but that are also available on the [Main Galaxy Toolshed](https://toolshed.g2.bx.psu.edu/). 
+Thus, it is possible to install them in a variety of Galaxy instances (some are already available elsewhere),
+including locally-administrated ones. 
+
+Want to have the W4M workflows on your favorite Galaxy instance or one on your own? Bellow are the steps to follow.
+
+#### Identify the Galaxy instance you want to use
+
+We, at W4M, do not provide support in Galaxy instance building and management. 
+Consequently, if you want to use our supported Galaxy workflows elsewhere than at usegalaxy.fr, 
+you need to have access to another already existing Galaxy instance. 
+
+In case you want to use your own Galaxy instance, you will need to have the required administration skills to deploy it 
+(or somebody around you available to deploy it for you). 
+Not sure what is needed to deploy such a Galaxy instance? 
+Check the [Galaxy Training Network](https://training.galaxyproject.org/training-material/learning-pathways/admin-training.html) 
+online materials: plenty of tutorials with hands-on to learn how to do so. 
+
+#### Identify the procedure to ask for additional Galaxy tools
+
+If you want to use W4M workflows on a Galaxy instance you do not manage yourself, 
+you need to identify whether there is a procedure to ask for additional tool installation. 
+In some cases, you have specific chanels (forum, contact e-mail) where to address your installation request. 
+Always follow the recommanded procedure of the Galaxy instance you want to use!
+
+If you want to use your own Galaxy instance but do not have the corresponding administration skills, 
+you will need to find someone arround you that have such skills to help you with the tool installation. 
+We, at W4M, do not provide such assistance, as we have limited human ressources. 
+
+#### Get the list of the W4M-supported Galaxy tools
+
+As we deploy the Galaxy tools we support and use on usegalaxy.fr, 
+and since this Galaxy instance implementation is publicly available, 
+you will find the list of all the tools we include in our W4M subdomain on Usegalaxy.fr's GitLab repository.
+
+In particular, you will find this [yml file](https://gitlab.com/ifb-elixirfr/usegalaxy-fr/tools) where ...
+
+#### Have a nice W4M journey!

tooluser.qmd

@@ -6,10 +6,12 @@
       type: table
       sort: "date"
       max-items: 100
-      fields: [galaxyref, link, title, author, W4M, doi]
+      fields: [title, author, W4M, Respository, doi-link]
+      field-links: [title, author]
+      table-hover: true
 ---
 
-The most effective way to master the use of our tools is by enrolling in our comprehensive training school ![](/images/W4E_icon.svg){height=1em}. Below you will find in-depth learning guides, providing you with the skills you need to leverage our tools seamlessly.
+The most effective way to master the use of our tools is by enrolling in our comprehensive [training school ![](/images/W4E_icon.svg){height=1em}](/news.qmd). Below you will find in-depth learning guides, providing you with the skills you need to leverage our tools seamlessly.
 
 If you have any questions or troubleshooting on Galaxy, one way to find an answer or solution is to visit the [IFB User Community](community.france-bioinformatique.fr/c/workflow4metabolomics/).
 
@@ -29,7 +31,7 @@ Access complete and interactive step-by-step guides by visiting the [![](https:/
 
 ## Galaxy ![](/images/W4M_icon.svg){height=1em} Instance
 
-Explore our [![](https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo_square.png){height=2em} Galaxy instance](https://workflow4metabolomics.usegalaxy.fr/) where each tool is accompanied by comprehensive support, including helpful documentation, examples, and references, ensuring that you have the resources you need.
+Explore our [![](https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo_square.png){height=2em} Galaxy instance](https://workflow4metabolomics.usegalaxy.fr) where each tool is accompanied by comprehensive support, including helpful documentation, examples, and references, ensuring that you have the resources you need.
 
 ## Workflows examples
 ::: {.panel-tabset}