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--- how_to:web:importresultfiles [2014/10/01 15:18]
193.48.0.3 créée
+++ how_to:web:importresultfiles [2016/07/05 16:53] (current)
193.48.0.3
@@ Line 2: / Line 2: @@
 The first thing to do in your brand new project is to import Result Files.
-To do so, Click on the “Import Result File” Button, in the toolbar of the project overview window or via a "right-click" on the Project node of the tree
-{{ :how_to:web:dse_import_result_file_btn.png?600 |}}
+There are many ways to open the dedicated tab:
+  * Right-click the //Imported Search Results// node, then click //Import result File//
+  * Right-click the project node, then click //Import result File//
+  * Right-click the project node, so that the project summary opens. Then click //Import result File// in this panel toolbar.
-You should then see this panel appear :
+{{ :how_to:web:dse_import_result_files.png?direct |}}
-{{ :how_to:web:dse_import_result_file_form.png?700 |}}
+A new tab opens and displays the following panel.\\
+Click on //Select result files// to browse and select them. The left side of the browsing window is meant for the directories. When you click on one of them, its content is shown on the main panel. Choose one or multiple files then click //Ok//.
-It allows you to select Result Files and set up following parameters for the import process :
+{{ :how_to:web:dse_import_result_files_add_files.png?nolink&direct |}}
+Then configure the following parameters:
   * Parameters
-    * Software Engine : the software which generated your interrogation file
+    * Software Engine: the software which generated your interrogation file
-    * Instrument : mass-spectrometer used for sample analysis
+    * Instrument: mass-spectrometer used for sample analysis
-    * Peaklist Software : the software used for the peaklist creation
+    * Peaklist Software: the software used for the peaklist creation
   * Decoy Parameters
-    * Decoy Strategy : TODO
+    * Decoy Strategy: The type of decoy search which was performed.
-    * Protein Match Decoy Rule : TODO
+      * "No Decoy Database": if the search was performed against a target database only.
+      * "Concatenated Decoy Database": if target and decoy sequences were merged into a single database.
+      * "Software Decoy": if the "Decoy" sequences were generated on-the-fly by your search engine.
+    * Protein Match Decoy Rule: for concatenated searches only. Select the rule to apply for the discrimination of target and decoy protein matches.
-  * Parser Parameters : according to your Software Engine, this will display some extra-parameters.
+  * Parser Parameters: according to your Software Engine, this will display some extra-parameters.
-    * Mascot :
+    * Mascot:
-      * Ion Score Cutoff : TODO
+      * Ion Score Cutoff: peptide matches with a score lower than this value won't be imported
-      * Subset Threshold : TODO
+      * Subset Threshold: the percentage of score between a given protein match and the master protein match (superset). Protein matches with a relative score lower than <code>Master_protein_score * (1-subset threshold)</code> won't be imported.
-      * Mascot Server URL : TODO
+    * Omssa:
-    * Omssa :
+      * User mod file: TODO
-      * User mod file : TODO
+      * PTM Composition File: TODO
-      * PTM Composition File : TODO
-  * Check Files before Import : let this checked to ensure that your files contain no errors. The server will perform a check operation before launching the import.
+\\
+\\
+You can now click on “Start Import” to launch the check and the import tasks.
+{{ :how_to:web:dse_project_tree_tasks.png?200|}}
+The server will check your files first, then the import itself will be launched automatically.
+You can follow the current state of your tasks by clicking on the Tasks button at the bottom of the Project Tree panel.
-In order to add files to your import selection, click on “Select Result File” to open the File Browser that will let you choose one or many result files to import :
+It will open the Tasks Panel, listing all the tasks you've been running in Proline.
-{{ :how_to:web:dse_import_result_file_select_file.png?direct |}}
-The left side let you browse the directories, and when you click on one of them, its content is shown on the main panel. Choose one or multiple files then click “Ok”.
-Back to the “Import Result File” window, you should now see your selection appear in the grid.
-Choose the instrument and the peaklist software corresponding to your files, and then select a “Decoy Strategy”. You can now click on “Start Import” to launch the check and the import tasks.
-The server will check your files first, then the import itself will be launched automatically.
-You can follow the current state of your tasks by clicking on the small cake in the bottom right corner of the desktop screen. It opens a small grid where you can see all your tasks.
-{{ :how_to:web:dse_import_result_file_tasks.png?direct |}}
+{{ :how_to:web:task_panel_import.png?direct |}}
 When a task is done, you are notified by a small message in the top of the screen, and you can see its status in the tasks window :
@@ Line 54: / Line 55: @@
 {{ :how_to:web:dse_import_finished.png?direct |}}
-All the Result Files you have imported are listed in the "Search Results" panel you can access by double-clicking the "Search Results" node in your project's tree.
+All the Result Files you have imported are listed in the //Imported Search Results// panel you can access by double-clicking the //Imported Search Results// node in your project tree.

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