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--- msangelworkflow [2015/10/13 17:24]
193.48.0.3
+++ msangelworkflow [2016/03/29 16:17] (current)
132.168.72.225
@@ Line 66: / Line 66: @@
 {{ :mascot_params.png?800 |}}
+\\
+\\
-Then save your new template by clicking //'Save parameters'//. You must provide your template a name, and an owner within Proline users.
+{{:save_params_template.png?450 |}}
+\\
+\\
-{{ :save_params_template.png?450 |}}
+Then save your new template by clicking //'Save parameters'//. \\
+You must provide your template a name, and an owner within Proline users.
+== . ==
 === Option B: Modify an existing template ===
@@ Line 139: / Line 146: @@
 In the '//Input data//' part, click on //Add files//. A file browser will open for you to select all your input files. It can be .RAW, .WIFF, or .MGF files. All input files must have the same extension.
-The default folder for this file browser can be set in //Setup (menu) -> Open setup dialog -> Preferences (first tab) -> File browsing (first section) -> Input files directory (first field)//.
+The default folder for this file browser can be set in //[[.:msangelInstallAndAdmin#|'Setup']] (menu) -> Open setup dialog -> Preferences (first tab) -> File browsing (first section) -> Input files directory (first field)//.
 As long as you task is not started, you can modify this list by adding more input files, or select and remove some (//Delete// button).
@@ Line 162: / Line 169: @@
 - //Ending options//: select the criterium to end up the task. It can be either a finite number of processed files, or a given date, or (if the two are selected) the first to be reached. It is currently impossible to launch a task in Real-time monitoring mode without ending parameters.
-== . ==
 === d. Design the workflow ===
@@ Line 172: / Line 179: @@
 The buttons at the top allow you to create and design new operations.
-{{:add_workflow_operation.png?600 |}}
+{{:add_workflow_operation.png?475 |}}
 **WARNING:** The operations order is crucial: the operations will be chained in this order, so it must be coherent with your file format, and in-between operations. For example, you must convert RAW files into MGF files before submitting them to Mascot, and must run a search on Mascot before import its results in Proline.\\
@@ Line 178: / Line 185: @@
 == File conversion ==
+{{ :file_conversion.png?1000 |}}
+Click on '//Add file conversion//'.
+Select the input format of your files (depending on the Schedule mode, it may be pre-selected), then the format in which they will be converted.
+You can then select a conversion tool. If none is displayed, then the conversion you wish to do is not yet handled by MS-Angel. The available tools are:
+  * ProteoWizard MsConvert (typically for RAW -> MGF conversions)
+  * ABSciex MS Data Converter (typically for WIFF -> MGF conversions).
+You can see and change the conversion settings by clicking //Options//.
+When using MsConvert, you can (and are recommanded to) use the Proline rule for generated spectrum titles by selecting '//Use Proline 1.0 parsing rule//'. Using this rule, your MGF file will contain all the information needed by Proline for further analysis.
 == Peaklist identification ==
+{{:pk_identification_croped.png?700 |}}
+Select the search engine(s) you desire for peaklist identification.
+For each, selected a parameter set by clicking the corresponding '//Select parameters//' button. When a template is chosen, its name and owner will be displayed, and you will be able to click '//See parameters//' to have a quick look at it.
+== . ==
+== . ==
 == Proline import ==
+{{:proline_import_croped.png?500 |}}
+This feature allows you to import each identification result in Proline, as soon as it is created.
+The parameters are the same than [[how_to:studio:importmascot|in ProlineStudio]] and [[.:how_to:web:importResultFiles|in Proline Web]].
+//Peaklist software//: the software that was used to create the peaklists (i.e. MGF files). If you used MS-Angel for this conversion, this value will be infered. (NB: If you used the option '//Use Proline 1.0 parsing rule//4, then select '//Proline 1.0//' here.)
+//Instrument configuration//: on which the samples were run
+//Decoy strategy//: if you ran a classic target/decoy search on Mascot, select '//Software Decoy//'.
+//Protein Match decoy rule//: these rules must be defined in Proline before (TODO: how to)
+//Ion score cutoff// and //Subset threshold// are optional.
+== . ==
 === e. Launch the task ===
+Click on '//RUN TASK//' at the bottom.
+{{ :run_task.png?1000 |}}
+{{ :task_submitted.png?450|}}
+\\
+A popup window will open to let you know if the task was well launched. Close this window, you will be redirected to the //Workflow History// tab.
+== . ==
 ==== 3. Visualize progression and results ====
+Two tabs are dedicated to tasks visualization.\\
+In the //Workflow History// tab, all tasks are displayed, and the progression of the workflow can be followed.\\
+In the //Identification History// tab, only tasks with a Peaklist Identification are displayed. The information given in this tab is related to the peaklist identification.
+=== Workflow history ===
+{{ :workflowhistory_enhanced.png?800 |}}
+In the tree at the left, all tasks are displayed with an icon pointing out the tasks status (running, succeeded, failed...). By double-clicking the task name (orange), the input files appear in the tree (yellow).\\
+A selected task can be cloned by clicking //Clone//.\\
+The displayed tasks can be filtered on their name using the tool circled in red above.
+The top-right parts (pale orange) are related to the tasks. It gives detailled information on the parameters (left) and workflow operations (right).
+The bottom-right table is search-related: one line per input file. Texts in blue are hyperlinks, offering much details on the search progression. Some columns may be shown or hidden ('+' icon, circled in yellow).
+{{ :copy_table.png?300|}}
+The table can be copied, without or without the column names (//headers//), by right-clicking on the table.\\
+You can also select only some cells to be copied (use the shift key to select a range of cells).
+You can switch to //Identification History// while keeping the focus on a given task. To do that, right click on the task name in the tree, then on '//Go to Mascot task//' / '//Go to OMSSA task//'.
+=== Identification history ===
+{{ :identification_history_enhanced.png?800 |}}
+The tasks in the tree are only those containing a Peaklist Identification in the workflow. So be aware that task number in the two history tabs may be different for a same task. If a search is run on //n// search engines, then there will be //n// associated identification tasks.
+The top-right part (pale orange) is related to the identification task: you can se the search parameter template that was used, and the details of these parameters (useful in case the template has been updated since).
+In te bottom-right table, search-related, you can see the details of the peaklist identification progression. For Mascot tasks, as in Mascot Daemon, you can click on a result file name (xxx.dat) to be redirected in your default web browser, on the Mascot result page.
+As for //Workflow History//, you can copy the table (whole or selected cells), show or hide columns, and filter the displayed tasks.
+You can also switch to the ///Workflow History// while keeping the focus on a given task; by right-clicking on the task name in the tree, and then on '//Go to Workflow task//'.

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