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5928 Commits
Author SHA1 Message Date
nekrutandClaude Opus 4.6 45c925755f Expand help text and add SVGs for apply rules, flat cross product, and nested cross product tools 
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 2026-03-02 02:34:28 +00:00
nekrutandClaude Opus 4.6 c26e201465 Expand help text and add/replace SVGs for relabel, sort, split, tag, unzip, and zip tools 
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 2026-03-02 02:22:06 +00:00
nekrutandClaude Opus 4.6 6377f2e322 Expand help text and add/replace SVGs for merge and nest collection tools 
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 2026-03-02 01:59:53 +00:00
nekrutandClaude Opus 4.6 72263595fd Expand help text and add SVG for keep success datasets tool 
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 2026-03-02 01:53:44 +00:00
nekrutandClaude Opus 4.6 cc07f516ca Expand help text and add SVG for harmonize two collections tool 
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 2026-03-02 01:34:17 +00:00
nekrutandClaude Opus 4.6 e63e2c9135 Expand help text and replace SVG for flatten collection tool 
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 2026-03-02 01:18:37 +00:00
nekrutandClaude Opus 4.6 bf9c5930d1 Expand help text and replace SVGs for filter empty, failed, and null tools 
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 2026-03-02 01:11:45 +00:00
nekrutandClaude Opus 4.6 766151da6a Expand help text and add SVG for filter from file tool 
Rewrite help with clearer descriptions of ABSENT/PRESENT modes,
add two-case SVG showing both filtering directions with dual
output collections (filtered + discarded).

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 2026-03-02 01:01:04 +00:00
nekrutandClaude Opus 4.6 430e30edc4 Expand help text and add SVG for extract dataset tool 
Add nested collection explanation with examples showing both flat
list extraction (case A) and list:list mapped extraction (case B).

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 2026-03-02 00:11:14 +00:00
nekrutandClaude Opus 4.6 b0f6eed662 Expand help text and add SVG for duplicate file to collection tool 
Add examples, workflow use case, and a clean SVG schematic showing
a single dataset being duplicated into a list collection.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 2026-03-01 23:16:55 +00:00
nekrutandClaude Opus 4.6 8ec98a9354 Replace build_list SVG with clean hand-coded diagram 
Replace the 207KB Inkscape-generated build_list.svg with a 10KB
hand-coded SVG matching the style of the sample sheet tool diagrams.
Uses abstract labels (Dataset 1, Dataset A, etc.) for all three cases.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 2026-03-01 23:12:58 +00:00
nekrutandClaude Opus 4.6 f841fc1e26 Expand help text and add SVG schematics for sample sheet tools 
Add "What is a sample sheet?" sections, concrete examples, and SVG
diagrams to both __CONVERT_SAMPLE_SHEET__ and __SAMPLE_SHEET_TO_TABULAR__
so newcomers understand what sample sheets are and when to use each tool.
Also adds the missing macros import to sample_sheet_to_tabular.xml.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 2026-03-01 23:02:59 +00:00
nekrutandClaude Opus 4.6 fea583da75 Update build_list help text and SVG image 
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 2026-03-01 16:51:32 +00:00
Matthias Bernt 91e06d84d5 Add tools to add nesting level to collection 
Given a list:X. If we want to map-over a tool that processes list:X
we need to restructure the list to list:list:X, where the inner lists
contain one element of X.

this can also be achieved by `Apply rules`, but the number of needed
clicks seems higher than desired?
 2025-09-19 16:59:05 +02:00
Dannon Baker 874040811e Drop out of date and unused fontawesome webfonts -- we don't use any of these with this mechanism anymore. 
I hope.
 2025-04-23 07:55:52 -04:00
Nate Coraor 235e4ce5c3 Update static handling for welcome.html to automatically load sample if 
the non-sample is not present, and for installed Galaxy. Fix robots.txt
and favicon which were not served at all due to middleware.
 2024-10-24 13:17:40 -04:00
Dannon Baker dfcc69eedf Disallow /tool_runner? in robots.txt 
This was getting spammed on main causing lots of extraneous jobs.  Might
need to follow up with updates to the tool panel to use direct tool
links like: https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0
 2024-10-17 10:18:56 -04:00
John Chilton 72baf52a56 Tool documentation for cross product tools. 2024-08-19 10:23:20 -04:00
Dannon Baker 8ca3a5b8f3 Drop unused autocomplete_tagging styles 2023-02-13 11:43:09 -05:00
Dannon Baker 1d78526aa2 Drop unused iconic_stroke* 2023-02-13 11:43:09 -05:00
Dannon Baker 6e527ca9ab Tours cleanup (this went with the swap to a custom tour driver) 2023-02-13 11:43:09 -05:00
Dannon Baker cf987666aa Drop wymeditor static 2023-02-13 11:43:09 -05:00
Dannon Baker b586a9de4b Drop style/base.css symlink -- nothing should use this anymore 2023-02-13 11:43:09 -05:00
Dannon Baker 8800bc82cd Update sample reference to static/style/base.css to dist 2023-02-07 16:51:22 -05:00
Martin Cech 063405a1cd replace the png favicon with svg version 
goes down from 16kb to 9kb and preserves all details

add padding to masthead logo

it now has no padding in the image itself

Add margin to svg

drop padding

since we decided to include it in logos

Slightly increase margin further
 2022-12-20 15:44:07 -08:00
guerler 91455ce2d2 Remove project from logo 2022-11-30 17:19:07 -05:00
guerler 95dadf3491 Rewrite masthead as composition, replace logo/text with logo only 2022-11-30 17:19:07 -05:00
David López 75c844b019 Merge pull request #14290 from mvdbeek/drop_root_controller_methods 
Drop root controller methods
 2022-07-12 19:08:32 +02:00
mvdbeek 4b20d96866 Remove legacy root controller methods 
And removes viewer applets that are hgighly unlikely to work and be
relevant. The tools are not installed on usegalaxy.org.
 2022-07-11 10:35:51 +03:00
Helena 53a803a9f2 Update robots.txt 2022-07-08 18:24:07 +02:00
John Chilton 7aa9ac539a Allow static components in tours. 2022-06-20 12:20:00 -04:00
guerler 4f6397f41e Adjust renaming in localization 2022-05-24 10:48:12 -04:00
nekrut 7facc8f82d updated tools and removed pngs 2021-07-16 15:39:21 -04:00
Anton Nekrutenko e1229dde03 SVGs 2021-07-16 15:32:56 -04:00
Anton Nekrutenko 451344048f image for buildList 2021-07-12 09:04:21 -04:00
nekrut 8e457fc15c border issue fixed 2021-01-08 15:52:04 -05:00
nekrut 480c123068 resizing 2021-01-08 15:44:04 -05:00
nekrut 78e4be04c8 new images 2021-01-08 15:39:28 -05:00
nekrut 8719332ff8 playing with resolution 2021-01-08 14:24:22 -05:00
nekrut 4a52111217 adding images and more cleaned tools 2021-01-06 17:53:41 -05:00
Dannon Baker 9388391a5a Fix two more broken symlinks (bugfix -- busted before this refactoring, in dev) 2020-08-11 10:26:06 -04:00
Dannon Baker 67c45422bd Update symlinks for images 2020-08-11 10:26:06 -04:00
Dannon Baker b7dd6acfa3 Drop static/src link -- everything in here goes through webpack and is bundled. If this breaks anything, we should really take a look at it. 2020-08-11 10:26:06 -04:00
Alexander OSTROVSKY f344dd85d3 parent 207f4c5fb0 
author Alexander OSTROVSKY <alexanderostrovsky@Caroline.local> 1565203601 -0400
committer Alexander OSTROVSKY <alexanderostrovsky@p-body.win.ad.jhu.edu> 1582640692 -0500

Notifications on job completion

JS lint for var notification

Altered to accomodate job failures and user cancellations

Added an icon to easily differentiate job success from failure

Tab updates when window is hidden.

Better completion message, removed console.log

Notification grammar, and linking tab icon change with notification permissions

tab fix

Tab resets on view

js lint
 2020-02-25 09:25:16 -05:00
Anthony Bretaudeau e11d091ea7 remove dead symlink 2020-01-31 17:17:05 +01:00
Dannon Baker 213bce31c2 Eliminate 'june_2007_style', squash some paths while working towards a flatter 'dist' exposure. Rebuild config (includes mulled stuff that I guess we forgot to build before?) 2020-01-23 13:01:59 -05:00
Dannon Baker 680bf6b7d2 Update two (old, deprecated...) symlinks to base.css 2020-01-23 13:01:59 -05:00
guerler 75d17a3332 Move icon png to static directory next to favicon.ico 2019-10-30 17:50:46 -04:00
guerler 9dc642a5b9 Use default button size 2019-06-17 20:12:55 -04:00
guerler 2bfe91f868 Increase default font-size by 0.05rem, use default font in default welcome page 2019-06-17 20:09:32 -04:00