Commit Graph
512 Commits
Author SHA1 Message Date
Kanwei Li 51da44adf9 trackster: Fix refactor breaking bam tracks. Only show draggable handle in editor mode. Update jQuery UI to 1.8.5 and add slider widget 2010-10-12 15:24:41 -04:00
Kanwei Li 2de6b5e055 trackster:
- Fix LineTrack axis labels not aligning consistently
- New image for draggable elements
- New slider that is rounded, easier to see and will go off-screen if smaller than the minimum width
- Added "Close overview" link when overview is showing
- Fix array_tree from recent refactoring
2010-10-08 16:56:45 -04:00
Jeremy Goecks abea9f8f76 Make VCF a first-class type in trackster. Added VCF data provider and VCF tracks type to trackster; new functionality is used to show reference base and alternate base for SNPs in VCF tracks. Also refactored data providers so that they inherit from a base provider. 2010-10-07 21:26:21 -04:00
Kanwei Li a889f76076 trackster: Can now reorder tracks inline. Put cancel button in modal dialogs to the left instead of right 2010-10-06 13:07:45 -04:00
Kanwei Li 6ba7f2811f New style for search boxes in grids. Grid items will no longer show outline when hovered upon if there are no actions to be performed. 2010-10-05 18:21:31 -04:00
Richard Burhans 8519dec03a updates to DAVID, LPS, and formatHelp help text 2010-10-05 11:59:36 -04:00
Kanwei Li 06b9b59b96 Make links in split menubuttons take the link instead of popping up the menu options. Use new menubutton style in data libraries and sharing_base. 2010-10-03 19:12:40 -04:00
Kanwei Li 52459bceb0 Refactored refresh_on_change javascript code to run in galaxy.base when the page is loaded. Fixed bug with autocomplete_select: when switching from a value within refresh_on_change_values to a value outside of it, the page did not refresh. Removed duplicate code from templates. 2010-10-01 16:20:34 -04:00
Kanwei Li 65a474b9a0 trackster: Move "Add Tracks" button to main pane, UI tweaks for overview 2010-09-29 13:56:09 -04:00
Richard Burhans 0cd1db87a2 Updates to help text for Human Genome Variation tools and formatHelp.html 2010-09-28 12:38:52 -04:00
Kanwei Li 0fbab45d14 trackster: Inline editing of configuration and removing of tracks, obsoleting the right editing panel. Improved appearance of overview box by adding a background for the scroll bar, and having a sliding window to indicate region shown. Added id numbers in front of API results for upcoming interactive script. 2010-09-23 20:00:58 -04:00
Richard Burhans 7dcc8b5f08 updated formatHelp and LPS help text 2010-09-21 19:41:25 -04:00
Ramkrishna Chakrabarty b8d1b02a55 interactivity bug fixed in mutation viz tool 2010-09-20 14:58:59 -04:00
Jeremy Goecks 6bfaa14643 Add tool search to workflow editor. Also standardize tool panel structure and style so that it is the same in both the main interface and in the workflow editor; workflow editor now uses styles in tool_menu.css as well. 2010-09-20 13:28:16 -04:00
Ramkrishna Chakrabarty 1bac740073 mutation viz tool
- now the tool requires the user to enter the specific columns indicating ref base, position, and start of a sample
- added an interactive zoom option. when this option is selected, the image can be zoomed in or out using the mouse wheel.
- fixed the firefox & opera problems in displaying the svg image
2010-09-20 12:07:09 -04:00
Kanwei Li a5ef9b53e2 - Refactored tagging/autocomplete JS, fixing bugs regarding leaving the tagging box
- Better packing for trackster when zoomed in as packing will be done on a w_scale basis instead of rounding to levels
- Move folder icon in data libraries to next to the text, rephrase suggestion on compression schemes
2010-09-17 17:51:11 -04:00
Richard Burhans c4ef1f8b5b Initial checkin of Human Genome Variation tools 2010-09-14 18:20:15 -04:00
Dannon Baker 5a28632683 Tweak to prevent workflow output indicator icon from getting out of sync. And repack. 2010-09-10 12:14:30 -04:00
Dannon Baker e629c020d2 Packed scripts. 2010-09-10 12:05:30 -04:00
Dannon Baker 74f9454636 Workflow changes-
Output flagging now has a third faded icon, and tooltip, and aligns properly on multiline outputs.
    ToolForm width now properly calculated, taking into account the length of input and output rows.
        -Max width is 250px, min is 150px.
    Output extensions are now properly separated by ', ' (including space) instead of just slammed together.
    Fixed a bug where a newly created node had no outputs array.
2010-09-10 11:59:38 -04:00
Jeremy Goecks 9e44caf592 UI improvements for annotating items: more descriptive messages and larger targets. 2010-09-08 17:52:01 -04:00
Kanwei Li dae04b0dae Clicking on a folder name in data libraries now expands the folder instead of displaying information/description, which is already in the name. Move fold icon next to folder name. Fix whitespace off by one 2010-09-08 17:20:16 -04:00
Dannon Baker 85e7c42ba8 Flagging of workflow outputs from within the workflow editor itself.
Hover over any output, click the asterisk to flag/unflag an output as a workflow-wide output.
2010-09-08 15:24:15 -04:00
Kanwei Li a541704a4a trackster: Fix drawing of features being cut off at bottom, added dropdown to track name for setting overview, and preferences in the future 2010-09-02 18:46:23 -04:00
Nate Coraor 44b0b1ca4d New config option to prevent Galaxy from retrying set_meta internally if it fails externally, and accompanying code to allow users to retry set_meta upon failure. 2010-09-02 10:22:51 -04:00
Kanwei Li 4ea8dd779b trackster: Changing display mode from "Auto" now fetches additional detail data and displays features. Displays error messages in canvas elements if present. Limit number of features displayed in one tile due to above feature. Fix bugs in visualization creation from form 2010-09-01 18:20:42 -04:00
Dannon Baker 894e1a43c3 Repacked workflow editor. 2010-08-31 11:58:59 -04:00
Dannon Baker a7aab68bbc Constrain connection to correct outputs when using ChangeDatatypeAction in workflow editor. 2010-08-30 18:48:08 -04:00
Dannon Baker 1d7a117da0 Workflow Fix- Enabled connection of nodes using ChangeDatatypeAction in the editor pane. 2010-08-30 18:38:35 -04:00
Kanwei Li ab8217d1e9 trackster: fix use of an old variable 2010-08-27 15:43:11 -04:00
Kanwei Li d8ad672ecf trackster: make "go-to" navigation inline, activated when chrom position is clicked. Drag-zoom overlay should now cover entire viewport (was missing a bit at bottom) 2010-08-26 19:04:55 -04:00
Kanwei Li 2b1d895ecf Repack js 2010-08-26 12:14:04 -04:00
Kanwei Li 4f291405f6 trackster: Overview track, viz cloning, "Go-to" specific location, UI fixes
- Each track now has an Overview checkbox that will set the initial chromosome-wide view of that track to become the overview
- Visualizations that users own or are shared with can now be cloned
- Go-to feature lets users go directly to a certain chrom (eg "chr1"), or chrom and position ("chr1:1-100,000,000")
- Fix double flushing when creating converter
- Line tracks display mode is now inline
- Use smaller font for tracks
- Fix web-kit bug where using scrollbar would also trigger viewport dragging
- Fix Line tracks jumping around when changing position
- Made default Line track height 80px from 100px
- Fix drag-zoom overlay appearing at top of header instead of Label track

- Minor grid refactoring
2010-08-26 12:12:32 -04:00
Dannon Baker 1d6896a316 Fix for the issue where multiple of the same action on separate outputs of a single tool were being overwritten as one. 2010-08-26 08:10:12 -04:00
Kanwei Li 4bd9e909b7 Use image_path for workflows and show_modal instead of relative paths 2010-08-20 15:00:52 -04:00
Dannon Baker 6803dea808 Workflow Output Tagging 2010-08-19 23:18:56 -04:00
Guruprasad Anada 12b9c486ea Adding wavelet analysis tools made by Zaky from Makova lab. 2010-08-16 18:30:37 -04:00
Ramkrishna Chakrabarty 37ff568432 Mutation visualization tool
Added svgfig egg
2010-08-12 14:21:59 -04:00
Kanwei Li 0ec45350aa trackster: Show counts for summary view by default, but only when text can fit in. Fix summary view off-by-pixel bug. Display Mode is now only initialized once and stays the same while switching chroms. 2010-08-09 20:01:02 -04:00
Kanwei Li 1898e7712b trackster: Add new dbkey column to viz tables, finish "Visualize in Trackster" button functionality
- Dbkey now shown in "Saved Visualizations" grid
- "Visualize in Trackster" icon in history pane for supported dataset now works, letting you add that dataset to an existing browser or to a new browser. Dbkey for existing browsers is also shown.
2010-08-03 15:10:30 -04:00
Jeremy Goecks 1e12562272 Add a ratings framework so that users can rate shared items. All sharable items--histories, workflows, datasets, visualizations, and pages--can be rated. Main framework components are (1) database tables for storing ratings; (2) UsesItemRatings mixin that supports rating items and obtaining an item's average rating; (3) controller methods to handle rating asynchronously; and (4) jQuery star rating plugin and supporting code that enables interactive item rating. (2) and (4) can be reused in the community space. 2010-08-03 11:45:25 -04:00
Kanwei Li c11b2ce4bc trackster:
- Fix Reference track incorrect display offset
- When no tracks exist in editor, show suggestion to add tracks
- Clicking "Visualize in Trackster" in history now shows a grid of current browsers, but actual adding is still work in progress
2010-07-28 18:51:32 -04:00
Kanwei Li c44e91819e trackster:
- Fix vertical scrolling with mouse quirkiness
- Intro screen asking to select a chrom when no chrom is selected
- Fix Reference tracks not hiding when there is no longer sequence to display
- Make embedded vis not overflow
- Fix drag-selecting region not working in embedded viz

make_style.py can now be run without parameters, which will default to the blue theme
2010-07-26 12:26:39 -04:00
Kanwei Li abf2404f02 trackster: remove mousewheel zoom (since scrolling window is more important), fix overview drag bug 2010-07-20 14:47:36 -04:00
Daniel Blankenberg 36f7bcb0c8 Modify tools contributed by Chungoo Park (cxp440@psu.edu) for Linear Discriminant Analysis, and drawing Receiver Operating Characteristic plots; add a new tool to 'Generate A Matrix for using PC and LDA'; remove redundant 'Principal Component Analysis' tool. 2010-07-16 14:52:52 -04:00
Kanwei Li 8e2331d652 Add image_path global variable to base_panels so that images can always have the right path. Fix image issues with trackster 2010-07-13 16:22:27 -04:00
Kanwei Li 7bc37cfcf7 Fixed creation of new tracks, missing template-generated css for trackster, add .DS_Store, *.rej and *.orig to hgignore 2010-07-12 14:59:11 -04:00
Jeremy Goecks f9911cae38 Pack scripts and update JS version. 2010-07-12 11:10:49 -04:00
Jeremy Goecks b3e1228cdc Make URLs for viz zoom in/out images relative. 2010-07-12 11:07:02 -04:00
Jeremy Goecks ea1c02e01e Move trackster.css to current stylesheets folder. 2010-07-12 10:20:56 -04:00