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--- msangelworkflow [2015/10/09 12:23]
193.48.0.3
+++ msangelworkflow [2016/03/29 16:17] (current)
132.168.72.225
@@ Line 33: / Line 33: @@
 We will follow the example of a user willing to launch a task executing :\\
-- the conversion of RAW acquisition files into peaklists,\\
+- the conversion of RAW acquisition files into MGF files (Mascot Generic Format),\\
 - a peaklist identification using Mascot,\\
 - the import of identification results into an existing Proline project.
@@ 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 111: / Line 118: @@
 === b. Define the task global parameters ===
-Consider the '**//Task//**' part of the '//New task//' tab.
+Consider the '//Task//' part of the '//New task//' tab.
 - First, give your task an arbitrary name. This is the name that will represent the task in the '//Workflow history//' and '//Identification history//' tabs.
@@ Line 133: / Line 140: @@
 == Mode 'Start now' ==
-{{:start_now.png?450 |}}
+{{:start_now.png?475 |}}
 In the '//Schedule//' part, select //Start now//.
@@ 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).
+== . ==
+== Mode 'Real time monitoring' ==
-== Mode '//Real time monitoring//' ==
+{{:real_time_monitoring.png?475 |}}
-{{:real_time_monitoring.png?450 |}} some text again
+In the '//Schedule//' part, select //Real time monitoring//.
+In the '//Input data//' part, you will be able to set up many parameters:
+- //Path to data folder//: the **absolute** path to the folder you want to monitor, e.g. where the input files will be created then handled by MS-Angel. You are advised to use the '//Browse//' button to select your folder.
+- //Optional wildcard for file(s) name//: you can use this textfield to filter the input files name and/or extension. A star means 'anything'. In the given example, only files whose name is ending with ".JPO.raw" will be taken into account. Only one expression can be described in this field (don't use comma-separated list of expressions). If you don't want to apply any filter, you can just leave this field blank or with '//*//' or the initial '//*.* //'.
+- //New files only//: if this option is checked, all files already existing before the task is launched will be ignored.
+- //Include sub-folder//: if this option is checked, files created in folders under the chosen data folder will be processed.
+- //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 ===
+Let's focus on the '//Workflow//' part.
+Here you will design the workflow applied on the input files. Three types of operations are currently available:\\
+- File conversion\\
+- Peaklist identification (on one or many search engines)\\
+- Proline import: import of Peaklist identification results in the Proline suite.
+The buttons at the top allow you to create and design new operations.
+{{: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.\\
+When you create an operation, it is placed at the end of the workflow. You can change its position by dragging and dropping it.
+== 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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