https://wiki.biouml.org/index.php?action=history&feed=atom&title=Generate_workflow_from_annotation_diagram_%28analysis%29 2026-04-21T02:13:37Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=Generate_workflow_from_annotation_diagram_(analysis)&diff=8876&oldid=prev 2020-12-09T11:15:02Z

<p>Automatic synchronization with BioUML</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 11:15, 9 December 2020</td> </tr><tr><td colspan="2" class="diff-lineno">Line 7:</td> <td colspan="2" class="diff-lineno">Line 7:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Plugin</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Plugin</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Biouml.plugins.genomeenhancer (plugin)|biouml.plugins.genomeenhancer (Genome Enhancer)]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Biouml.plugins.genomeenhancer (plugin)|biouml.plugins.genomeenhancer (Genome Enhancer)]]</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">==== Description ====</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">This method generates and runs the Genome Enhancer workflow for multi-omics data processing based on the selected conditions: data categories from annotation diagram, studied diseases and tissue type from which the data was retrieved (optional parameter).</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Additional parameters (expert options) of this method allow selection of certain steps of this analysis to be skipped:</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">If ''run workflow'' is selected, the generated workflow will be executed, otherwise, the method will create the workflow, but will not execute it.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">If ''unique output'' is selected, the results of this method will be saved into a new folder (adding a consequent number to the name of the folder: (1), (2), etc, in case the folder with the same name already exists), otherwise the method will overwrite the results contained in the originally specified output folder.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">If ''generate report'' is selected, the method will create a new Genome Enhancer report (Full story and Brief tale reports).</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">If ''notify when completed'' is selected, the method will send you an email once it will finish the analysis.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">If ''add MTB report'' is selected, then MTB report will be generated. Please note that MTB report can be generated only for input genomics data and for not more than two conditions. If one of these rules is violated, the MTB report will not be generated.</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Parameters: ====</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Parameters: ====</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 15:</td> <td colspan="2" class="diff-lineno">Line 30:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Diseases''' – Diseases.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Diseases''' – Diseases.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Choose your data for analysis''' – Choose your data for analysis</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Choose your data for analysis''' – Choose your data for analysis</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* '''Baseline''' (expert) – Use baseline if 2 and more conditions are selected</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Run workflow''' (expert) – Run workflow</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Run workflow''' (expert) – Run workflow</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Unique output''' (expert) – Unique output</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Unique output''' (expert) – Unique output</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Generate report''' (expert) – Generate report</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Generate report''' (expert) – Generate report</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* '''<del class="diffchange diffchange-inline">outPath</del>''' (expert) – <del class="diffchange diffchange-inline">outPath</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* '''<ins class="diffchange diffchange-inline">Notify when completed</ins>''' (expert) – <ins class="diffchange diffchange-inline">Send e-mail notification when analysis is finished</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* '''Add MTB report''' (expert) – Create Molecular Tumor Board report on genomics data if selected disease can be classified as cancer.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* '''Result path''' (expert) – Path to folder with results</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Analyses]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Analyses]]</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=Generate_workflow_from_annotation_diagram_(analysis)&diff=7779&oldid=prev 2019-03-12T09:33:29Z

<p>Protected &quot;<a href="/index.php/Generate_workflow_from_annotation_diagram_(analysis)" title="Generate workflow from annotation diagram (analysis)">Generate workflow from annotation diagram (analysis)</a>&quot;: Autogenerated page (‎[edit=sysop] (indefinite))</p> <table class='diff diff-contentalign-left'> <tr style='vertical-align: top;'> <td colspan='1' style="background-color: white; color:black;">← Older revision</td> <td colspan='1' style="background-color: white; color:black;">Revision as of 09:33, 12 March 2019</td> </tr></table>

WikiBot https://wiki.biouml.org/index.php?title=Generate_workflow_from_annotation_diagram_(analysis)&diff=7775&oldid=prev 2019-03-12T09:33:27Z

<p>Automatic synchronization with BioUML</p> <p><b>New page</b></p><div>;Analysis title<br /> :[[File:Default-analysis-icon.png]] Generate workflow from annotation diagram<br /> ;Provider<br /> :[[Biosoft]]<br /> ;Class<br /> :{{Class|biouml.plugins.genomeenhancer.megaworkflow.GenerateWorkflow}}<br /> ;Plugin<br /> :[[Biouml.plugins.genomeenhancer (plugin)|biouml.plugins.genomeenhancer (Genome Enhancer)]]<br /> <br /> ==== Parameters: ====<br /> <br /> * '''Data source''' – Data source.<br /> * '''Species''' – Species.<br /> * '''Tissue''' – Tissue.<br /> * '''Diseases''' – Diseases.<br /> * '''Choose your data for analysis''' – Choose your data for analysis<br /> * '''Run workflow''' (expert) – Run workflow<br /> * '''Unique output''' (expert) – Unique output<br /> * '''Generate report''' (expert) – Generate report<br /> * '''outPath''' (expert) – outPath<br /> <br /> [[Category:Analyses]]<br /> [[Category:Genome enhancer (analyses group)]]<br /> [[Category:Biosoft analyses]]<br /> [[Category:Autogenerated pages]]</div>

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