msangelworkflow
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msangelworkflow [2015/10/14 11:33] 193.48.0.3 |
msangelworkflow [2016/03/29 16:17] (current) 132.168.72.225 |
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| 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. | 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). | 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). | ||
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| {{:proline_import_croped.png?500 |}} | {{:proline_import_croped.png?500 |}} | ||
| This feature allows you to import each identification result in Proline, as soon as it is created. | 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:importmascot|in ProlineWeb]]. | + | 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.) | //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.) | ||
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| ==== 3. Visualize progression and results ==== | ==== 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 === | === 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 === | ||
| + | |||
| + | {{ :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//'. | ||
msangelworkflow.1444815183.txt.gz · Last modified: 2015/10/14 11:33 by 193.48.0.3
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