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Release 3.2 #6

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Release 3.2 #6

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97734ed
update tools
lecorguille Jul 3, 2019
0ee36f5
update GCMS tools
lecorguille Jul 3, 2019
bb7015c
disable install_resolver_dependencies
lecorguille Jul 3, 2019
4688e59
fix metams_plot
lecorguille Jul 3, 2019
dcae02e
disable install_resolver_dependencies again
lecorguille Jul 3, 2019
b012315
fix
lecorguille Jul 3, 2019
0528de5
update welcome
lecorguille Jul 3, 2019
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49 changes: 3 additions & 46 deletions static/welcome.html
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</div>

<div class="donemessagelarge">
<h1>Current version : 3.2 - 19/09/2018</h1>
<h1>Current version : 3.2 - 03/07/2019</h1>
<strong>Publication:</strong> Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Thévenot and Christophe Caron (2014). <strong>Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics</strong>. Bioinformatics <a href="http://bioinformatics.oxfordjournals.org/content/early/2014/12/18/bioinformatics.btu813" target="_blank">doi:10.1093/bioinformatics/btu813</a><br/><br/>
<b>Help and support: <a href="mailto:[email protected]">[email protected]</a></b>
</div>

<div class="infomessagelarge">
<h2>Latest news</h2>
<ul>
<li>UPGRADE/NEW - LCMS/Preprocessing - xcms.* (3.0.0): upgrade the xcms version from 1.46.0 to 3.0.0. Note that there aren't any retro compatibility between xcms1.46.0 and xcms3.0.0. You have to run the whole workflow from scratch.</li>
<li>NEW in Docker - ALL/Statistics - mixmodel ANOVA for repeated measures statistics</li>
<li>NEW in Docker - ALL/Statistics - ASCA Splitting of the total variance into independent blocks according to the experimental factors and multivariate analysis (SCA) of each block</li>
<li>NEW in Docker - LCMS/Annotation - bank_inhouse search by accurate mass (and by Retention time) on a local bank</li>
<li>NEW in Docker - NMR/Annotation - NMR_Annotation Annotation of complex mixture NMR spectra and metabolite proportion estimation</li>
<li>UPGRADE
<ul>
<li>LCMS/Preprocessing - camera.*</li>
<li>FIAMS/Preprocessing - Profia</li>
<li>GCMS/Preprocessing - MetaMS</li>
<li>NMR/Preprocessing - NMR preprocessing, NMR alignment, NMR bucketing</li>
<li>ALL/Quality Metric - Normalization, Transformation, Quality Metrics, Multilevel, </li>
<li>ALL/Statistics - Univariate, Multivariate, Anova, </li>
<li>LCMS/Annotation - HMDB MS search, Lipidmaps</li>
</ul>
</li>
</ul>
</div>


<div id="W4M">
<div id="accordion">
<div> <!-- class="collapseclose">-->
<h3>Tutorials</h3>
<div id="tutorial_accordion">
<h4>HOW TO</h4>
<div>
<table style="width: 100%;" border="1" cellspacing="1" cellpadding="1"><thead><tr><th>CATEGORY</th><th>FIELD</th><th>Description</th><th>PDF</th></tr></thead><tbody><tr><td style="width: 150px;">Galaxy</td><td style="width: 150px;">&nbsp;</td><td style="width: 369px;">Prepare input datasets</td><td style="width: 100px;"><a href="http://abims.sb-roscoff.fr/mypydio/data/public/aaeb31.php?dl=true">Download</a></td></tr><tr><td style="width: 150px;">Galaxy</td><td style="width: 150px;">&nbsp;</td><td style="width: 369px;">Import datasets</td><td style="width: 100px;"><a href="http://abims.sb-roscoff.fr/mypydio/data/public/8880e7.php?dl=true">Download</a></td></tr><tr><td style="width: 150px;">Galaxy</td><td style="width: 150px;">&nbsp;</td><td style="width: 369px;">Cleanup datasets</td><td style="width: 100px;"><a href="http://abims.sb-roscoff.fr/mypydio/data/public/f0fd7c.php?dl=true">Download</a></td></tr><tr><td style="width: 150px;">Galaxy</td><td style="width: 150px;">&nbsp;</td><td style="width: 369px;">Build And Configure A Workflow</td><td style="width: 100px;"><a href="http://abims.sb-roscoff.fr/mypydio/data/public/9bc79d.php?dl=true">Download</a></td></tr><tr><td style="width: 150px;">Galaxy</td><td style="width: 150px;">&nbsp;</td><td style="width: 369px;">Share Histories And Workflows</td><td style="width: 100px;"><a href="http://abims.sb-roscoff.fr/mypydio/data/public/8e8802.php?dl=true">Download</a></td></tr><tr><td style="width: 150px;">Preprocessing</td><td style="width: 150px;">LC-MS</td><td style="width: 369px;">Perform Preprocessing using XCMS</td><td style="width: 100px;"><a href="http://abims.sb-roscoff.fr/mypydio/data/public/084ad1.php?dl=true">Download</a></td></tr><tr><td style="width: 150px;">Quality Control</td><td style="width: 150px;">Common</td><td style="width: 369px;">Format Data For Postprocessing</td><td style="width: 100px;"><a href="http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToFormatDataForPostprocessing_v02.pdf">Download</a></td></tr><tr><td style="width: 150px;">Batch correction</td><td style="width: 150px;">LC-MS and GC-MS</td><td style="width: 369px;">Perform Drift And Batch Correction</td><td style="width: 100px;"><a href="http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformDriftAndBatchCorrection_v02.pdf">Download</a></td></tr><tr><td style="width: 150px;">Statistics</td><td style="width: 150px;">Common</td><td style="width: 369px;">Perform Univariate Analyzes</td><td style="width: 100px;"><a href="http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformUnivariateAnalyzes_v02.pdf">Download</a></td></tr><tr><td style="width: 150px;">Statistics</td><td style="width: 150px;">Common</td><td style="width: 369px;">Perform Multivariate Analyzes</td><td style="width: 100px;"><a href="http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformMultivariateAnalyzes_v02.pdf">Download</a></td></tr><tr><td style="width: 150px;">Annotation</td><td style="width: 150px;">LC-MS</td><td style="width: 369px;">Perform LCMS Annotations</td><td style="width: 100px;"><a href="http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformAnnotations_v05.pdf">Download</a></td></tr><tr><td style="width: 150px;">Annotation</td><td style="width: 150px;">GC-MS</td><td style="width: 369px;">Use NIST</td><td style="width: 100px;"><a href="http://application.sb-roscoff.fr/download/w4m/howto/w4m_HowToUseNIST_V01.pdf">Download</a></td></tr></tbody></table>

<br/><hr/>
<h5 id="single_files">Use single files as input and run xcmsSet in parallel</h5>
<video style="align:center;max-width:1280px;width:95%;" controls="controls" scale="tofit" >
<source src="http://download.workflow4metabolomics.org/docs/170510_galaxy_xcms_dataset_collection.m4v" type="video/mp4">
</video>
<a href="http://download.workflow4metabolomics.org/docs/170510_galaxy_xcms_dataset_collection.m4v">Download the video</a>
</div>
<h4>W4M courses 2015</h4>
<div>
<table style="width: 100%;" border="1" cellspacing="1" cellpadding="1"><thead><tr><th scope="col">W4M courses 2015</th><th scope="col">Author(s)</th><th scope="col">PDF</th></tr></thead><tbody><tr><td>Course presentation</td><td>Christophe Caron, Franck Giacomoni</td><td><a href="/sites/workflow4metabolomics.org/files/files/00_course_presentation_fg-cc_20150918.pdf" target="_blank">Download</a></td></tr><tr><td>Initiation</td><td>Gildas Le Corguillé, Misharl Monsoor, Marion Landi</td><td><a href="/sites/workflow4metabolomics.org/files/files/galaxy-init-1.05_printable.pdf" target="_blank">Download</a></td></tr><tr><td>LC-MS -&nbsp;Pre-processing (xcms)</td><td>W4M Core Team</td><td><a href="/sites/workflow4metabolomics.org/files/files/w4m_xcms_CAMERA_LC-MS.pdf" target="_blank">Download</a></td></tr><tr><td>MS data processing - Filtering and correcting data</td><td>W4M Core Team</td><td><a href="/sites/workflow4metabolomics.org/files/files/MS_data_processing.pdf" target="_blank">Download</a></td></tr><tr><td>Using&nbsp;Galaxy4Metabolomics -&nbsp;W4M table format for&nbsp;Galaxy</td><td>W4M Core Team</td><td><a href="/sites/workflow4metabolomics.org/files/files/w4m_TableFormatForGalaxy_150908.pdf" target="_blank">Download</a></td></tr><tr><td>How to check the format&nbsp;of the 3 .tsv tables</td><td>Etienne Thévenot</td><td><a href="/sites/workflow4metabolomics.org/files/files/w4m_HowToPerformStatisticalAnalysis_Appendix_CheckFormat_150923.pdf" target="_blank">Download</a></td></tr><tr><td>How to perform statistical analysis ? - Introduction</td><td>Etienne Thévenot, Marie Tremblay-Franco, Mélanie Pétéra, Gildas Le Corguillé</td><td><a href="/sites/workflow4metabolomics.org/files/files/w4m_HowToPerformStatisticalAnalysis_1_Introduction_150923.pdf" target="_blank">Download</a></td></tr><tr><td>How to perform statistical analysis ? - Exploratory data analysis</td><td>Etienne Thévenot, Mélanie Pétéra, Jean-François Martin, Gildas Le Corguillé</td><td><a href="/sites/workflow4metabolomics.org/files/files/w4m_HowToPerformStatisticalAnalysis_2_ExploratoryDataAnalysis_150923.pdf" target="_blank">Download</a></td></tr><tr><td>How to perform statistical analysis ? -&nbsp;PCA analysis and&nbsp;(O)PLS(-DA) modelling</td><td>Etienne Thévenot</td><td><a href="/sites/workflow4metabolomics.org/files/files/w4m_HowToPerformStatisticalAnalysis_4_MultivariateModelling_150923.pdf" target="_blank">Download</a></td></tr><tr><td>Les banques d'annotation - Annotation</td><td>Yann Guitton, Franck Giacomoni</td><td><a href="/sites/workflow4metabolomics.org/files/files/W4M_Annotation_banques_annotation.pdf" target="_blank">Download</a></td></tr></tbody></table><p>&nbsp;</p>
</div>
</div>
</div>
</div>
<hr />
<div width="auto" align="center">
<img src="W4M/workflow_all_HD_color_2.0.png" style="max-width:1500px;width:95%;" /><br/>
<img src="W4M/bigpicture.png" style="max-width:1500px;width:95%;" /><br/>
<hr />
<img src="W4M/workflow_community_HD_2.0.png" style="max-width:1000px;width:95%;" />
</div>
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11 changes: 8 additions & 3 deletions tool_list.yaml
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Expand Up @@ -3,7 +3,7 @@
api_key: admin
galaxy_instance: http://127.0.0.1:8080/
install_repository_dependencies: true
install_resolver_dependencies: true
install_resolver_dependencies: false
install_tool_dependencies: false

tools:
Expand Down Expand Up @@ -72,7 +72,12 @@ tools:
owner: yguitton
tool_panel_section_id: 'preprocessing_GCMS'
revisions:
- 'c75532b75ba1' # v2.1.1
- 'c10824185547' # v3.0.0
- name: metams_plot
owner: workflow4metabolomics
tool_panel_section_id: 'preprocessing_GCMS'
revisions:
- 'b60dc620bd14' # v1.0.0

## NMR
- name: nmr_preprocessing
Expand Down Expand Up @@ -132,7 +137,7 @@ tools:
owner: ethevenot
tool_panel_section_id: 'statistics_ALL'
revisions:
- '526f8258e8a' # v2.3.10
- '5526f8258e8a' # v2.3.10
- name: anova
owner: lecorguille
tool_panel_section_id: 'statistics_ALL'
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