Merge branch 'galaxyproject:main' into FPE_SeuratTools

CONTRIBUTORS.yaml

@@ -541,7 +541,7 @@ eancelet:
 
 elichad:
     name: Eli Chadwick
-    email: eli.chadwick@stfc.ac.uk
+    email: eli.chadwick@manchester.ac.uk
     orcid: 0000-0002-0035-6475
     joined: 2022-11
 

_config.yml

@@ -27,9 +27,11 @@ small_logo: "assets/images/GTN-60px.png"
 help_url: https://help.galaxyproject.org/
 other_languages: #"fr, ja, es, pt, ar"
   en: English
+  de: Deutsch
+  es: Español
+  zh-CN: 中文
   fr: Français
   ja: 日本語
-  es: Español
   pt: Português
   ar: العربية
 
@@ -111,11 +113,12 @@ icon-tag:
   galaxy-chart-select-data: fas fa-database
   galaxy-clear: fas fa-times-circle
   galaxy-columns: fas fa-columns
+  galaxy-multihistory: fas fa-columns
   galaxy-cross: fas fa-times
   galaxy-dataset-map: fas fa-sitemap
   galaxy-delete: fas fa-trash
   galaxy-dropdown: fas fa-caret-down
-  galaxy-history-options: fas fa-caret-down # Replaces gear.
+  galaxy-history-options: fas fa-bars # Replaces gear, fa-caret-down
   galaxy-eye: far fa-eye
   galaxy-gear: fas fa-cog
   galaxy-history: fas fa-columns

_includes/resource-handson.html

@@ -19,10 +19,10 @@
             <span class="sr-only">Toggle Dropdown</span>
         </a>
         <ul class="dropdown-menu">
-        {% assign translations = material.translations.tutorial | size %}
+        {% assign translations = include.material.translations.tutorial | size %}
         {% if translations > 0 %}
           <li class="dropdown-item"><strong>Curated translations</strong></li>
-           {% for lang in material.translations.tutorial %}
+           {% for lang in include.material.translations.tutorial %}
             <li class="dropdown-item">
             <a class="dropdown-item" hreflang="{{ lang }}" href="{{ site.baseurl }}/topics/{{ include.material.topic_name }}/tutorials/{{ include.material.tutorial_name }}/tutorial_{{lang | upcase }}.html" title="{{ lang }}">
                 {{language[lang]}}
@@ -32,18 +32,18 @@
 
           <hr/>
         {% endif %}
-         <li class="dropdown-item"><strong>Automatic translations</strong></li>
-        {% for lang in language %}{% unless lang[0] == 'en' %}
+        <li class="dropdown-item"><strong>Automatic translations</strong></li>
+        {% for lang in site.other_languages %}{% unless lang[0] == 'en' %}
 	<li class="dropdown-item">
-            <a class="dropdown-item" hreflang="{{ lang[0] }}" href="https://translate.google.com/translate?hl=jp&sl=en&tl={{ lang[0] }}&u=https%3A%2F%2Ftraining.galaxyproject.org%2Ftopics%2F{{ include.material.topic_name }}%2Ftutorials%2F{{ include.material.tutorial_name }}%2Ftutorial.html&edit-text=&act=url" title="{{ inst[0] }}">
-                {{ lang[1] }}
-            </a>
+		<a class="dropdown-item" hreflang="{{ lang[0] }}" href="https://training-galaxyproject-org.translate.goog/training-material/topics/{{ include.material.topic_name }}/tutorials/{{ include.material.tutorial_name }}/tutorial.html?_x_tr_sl=en&_x_tr_tl={{ lang[0] }}&_x_tr_hl=en&_x_tr_pto=wapp" title="{{ inst[0] }}">
+			{{ lang[1] }}
+		</a>
 	</li>
         {% endunless %}{% endfor %}
 	<li class="dropdown-item">
-        <a class="dropdown-item" href="https://translate.google.com/translate?hl=jp&sl=en&tl=&u=https%3A%2F%2Ftraining.galaxyproject.org%2Ftopics%2F{{ include.material.topic_name }}%2Ftutorials%2F{{ include.material.tutorial_name }}%2Ftutorial.html&edit-text=&act=url" title="{{ inst[0] }}">
-            More Languages
-        </a>
+		<a class="dropdown-item" href="https://training-galaxyproject-org.translate.goog/training-material/topics/{{ include.material.topic_name }}/tutorials/{{ include.material.tutorial_name }}/tutorial.html?_x_tr_sl=en&_x_tr_tl=fr&_x_tr_hl=en&_x_tr_pto=wapp" title="{{ inst[0] }}">
+			More Languages
+		</a>
 	</li>
     </ul>
 </div>

_includes/resource-slides.html

@@ -25,23 +25,23 @@
         {% endif %}
 
         <li class="dropdown-item"><strong>Automatic translations</strong></li>
-        {% for lang in language %}{% unless lang[0] == 'en' %}
-		<li class="dropdown-item">
-            <a class="dropdown-item" hreflang="{{ lang[0] }}" href="https://translate.google.com/translate?hl=jp&sl=en&tl={{ lang[0] }}&u=https%3A%2F%2Ftraining.galaxyproject.org%2Ftopics%2F{{ include.material.topic_name }}%2F{{subfolder}}%2F{{ include.material.tutorial_name }}%2Fslides.html&edit-text=&act=url" title="{{ inst[0] }}">
-                {{ lang[1] }}
-            </a>
-		</li>
+        {% for lang in site.other_languages %}{% unless lang[0] == 'en' %}
+	<li class="dropdown-item">
+		<a class="dropdown-item" hreflang="{{ lang[0] }}" href="https://training-galaxyproject-org.translate.goog/training-material/topics/{{ include.material.topic_name }}/tutorials/{{ include.material.tutorial_name }}/slides.html?_x_tr_sl=en&_x_tr_tl={{ lang[0] }}&_x_tr_hl=en&_x_tr_pto=wapp" title="{{ inst[0] }}">
+			{{ lang[1] }}
+		</a>
+	</li>
         {% endunless %}{% endfor %}
-		<li class="dropdown-item">
-        <a class="dropdown-item" href="https://translate.google.com/translate?hl=jp&sl=en&tl=&u=https%3A%2F%2Ftraining.galaxyproject.org%2Ftopics%2F{{ include.material.topic_name }}%2F{{subfolder}}%2F{{ include.material.tutorial_name }}%2Fslides.html&edit-text=&act=url" title="{{ inst[0] }}">
-            More Languages
-        </a>
-		</li>
+	<li class="dropdown-item">
+		<a class="dropdown-item" href="https://training-galaxyproject-org.translate.goog/training-material/topics/{{ include.material.topic_name }}/tutorials/{{ include.material.tutorial_name }}/slides.html?_x_tr_sl=en&_x_tr_tl=fr&_x_tr_hl=en&_x_tr_pto=wapp" title="{{ inst[0] }}">
+			More Languages
+		</a>
+	</li>
 
 	<li class="dropdown-item">
-	<a class="btn btn-default topic-icon" href="{{ site.baseurl }}/topics/{{ include.material.topic_name }}/{{subfolder}}/{{ include.material.tutorial_name }}/slides-plain.html" aria-label="more accessible, plain text slides">
-		{% icon text-document aria=false %} Plain text slides
-	</a>
+		<a class="btn btn-default topic-icon" href="{{ site.baseurl }}/topics/{{ include.material.topic_name }}/{{subfolder}}/{{ include.material.tutorial_name }}/slides-plain.html" aria-label="more accessible, plain text slides">
+			{% icon text-document aria=false %} Plain text slides
+		</a>
 	</li>
     </ul>
 </div>

api/swagger.json

@@ -41,7 +41,13 @@
         "responses": {
           "200": {
             "description": "successful operation",
-            "content": "application/csv"
+            "content": {
+              "application/csv": {
+                "schema": {
+                  "type": "string"
+                }
+              }
+            }
           }
         }
       }
@@ -55,7 +61,13 @@
         "responses": {
           "200": {
             "description": "successful operation",
-            "content": "application/json"
+            "content": {
+              "application/json": {
+                "schema": {
+                  "type": "string"
+                }
+              }
+            }
           }
         }
       }
@@ -376,10 +388,10 @@
             "name": "toolId",
             "in": "path",
             "example": "toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate",
-            "description": "Tool ID WITHOUT the version component!!",
+            "description": "Tool ID WITHOUT the version component!! Also when you call it properly you do NOT need to encode the /.",
             "required": true,
             "schema": {
-              "type": "string"
+              "type": "object"
             }
           }
         ],

bin/check-url-persistence.sh

@@ -1,4 +1,8 @@
 #!/bin/bash
+if [[ ! -f /tmp/2021.txt ]]; then
+	curl --silent https://training.galaxyproject.org/archive/2021-02-01/sitemap.xml | sed 's|<url>|\n|g' | grep '<loc>[^<]*</loc>' -o | sed 's/<loc>//;s/<\/loc>//' | sed 's|archive/2021-02-01|training-material|g'  > /tmp/2021.txt
+fi
+
 if [[ ! -f /tmp/2022.txt ]]; then
 	curl --silent https://training.galaxyproject.org/archive/2022-01-01/sitemap.xml | sed 's|<url>|\n|g' | grep '<loc>[^<]*</loc>' -o | sed 's/<loc>//;s/<\/loc>//' | sed 's|archive/2022-01-01|training-material|g'  > /tmp/2022.txt
 fi
@@ -7,10 +11,17 @@ if [[ ! -f /tmp/2024.txt ]]; then
 	curl --silent https://training.galaxyproject.org/archive/2024-01-01/sitemap.xml | sed 's|<url>|\n|g' | grep '<loc>[^<]*</loc>' -o | sed 's/<loc>//;s/<\/loc>//' | sed 's|archive/2024-01-01|training-material|g'  > /tmp/2024.txt
 fi
 
+
+if [[ ! -f /tmp/2099.txt ]]; then
+	curl --silent https://training.galaxyproject.org/training-material/sitemap.xml | sed 's|<url>|\n|g' | grep '<loc>[^<]*</loc>' -o | sed 's/<loc>//;s/<\/loc>//' > /tmp/2099.txt
+fi
+
 # No guarantees of API or data-file persistence
 # 1fe4d7d92e5ea5a5794cbe741eadb96a74511261
-cat /tmp/202*.txt | grep -v '/api/' | grep -v '/by-tool/'  | grep -v '/hall-of-fame/' | \
+cat /tmp/20*.txt | sort -u | \
+	grep -v '/api/' | grep -v '/by-tool/'  | grep -v '/hall-of-fame/' | \
 	grep -v '/badges/' | \
+	grep --extended-regexp -v 'krona_?[a-z]*.html' | \
 	grep -v '/transcriptomics/tutorials/ref-based/faqs/rnaseq_data.html' | \
 	grep -v '/topics/data-management/' | \
 	grep -v 'training-material/tags/' | grep -v 'data-library'| \

bin/news.rb

@@ -37,7 +37,7 @@
   'wg-goat' => {
     server: 'https://matrix.org',
     room: '!UQXYBSjdrLHcWgegmg:gitter.im',
-  }
+  },
   'hub-social' => {
     server: 'https://matrix.org',
     room: '!gegHcnUCDklLbtVQor:matrix.org',

faqs/galaxy/activity_bar_how_to_enable.md

@@ -0,0 +1,18 @@
+---
+title: How to enable the Activity Bar
+description: This FAQ demonstrates how to enable the activity bar within the Galaxy interface
+box_type: tip
+layout: faq
+contributors: [nekrut]
+---
+
+If you do not see the Activity Bar it can be enabled as follows:
+
+1. Click on the "**User**" link at the top of the Galaxy interface
+2. Select "**Preferences**"
+3. Scroll down and click on "**Manage Activity Bar**"
+4. Toggle the "**Enable Activity Bar**" switch and voila!
+
+   ![The four steps described above are shown visually]({% link shared/images/activity_bar_how_to_enable.svg %})
+
+<!-- Original drawing = https://docs.google.com/drawings/d/1yynqEiV66F8idKH5JwTG-4ASuqK62thIwHeCMHRuupg/edit?usp=sharing -->

faqs/galaxy/datasets_change_datatype.md

@@ -4,11 +4,11 @@ description: Galaxy will try to autodetect the datatype of your files, but you m
 area: datasets
 box_type: tip
 layout: faq
-contributors: [bebatut,nsoranzo,hexylena,shiltemann,ajadi-abiola,lldelisle]
+contributors: [bebatut,nsoranzo,hexylena,shiltemann,ajadi-abiola,lldelisle,nekrut]
 ---
 
 * Click on the {% icon galaxy-pencil %} **pencil icon** for the dataset to edit its attributes
-* In the central panel, click on the {% icon galaxy-gear %} **Convert** tab on the top
-* In the lower part {% icon galaxy-chart-select-data %} **Datatypes**, select {% if include.datatype %}`{{ include.datatype }}`{% else %} your desired datatype {% endif %}
-  - tip: you can start typing the datatype into the field to filter the dropdown menu
+* In the central panel, click {% icon galaxy-chart-select-data %} **Datatypes** tab on the top
+* In the {% icon galaxy-chart-select-data %} **Assign Datatype**, select {% if include.datatype %}`{{ include.datatype }}`{% else %} your desired datatype {% endif %} from "*New type*" dropdown  
+  - Tip: you can start typing the datatype into the field to filter the dropdown menu
 * Click the **Save** button

faqs/galaxy/datasets_change_dbkey.md

@@ -4,10 +4,14 @@ description: You can tell Galaxy which dbkey (e.g. reference genome) your datase
 area: datasets
 box_type: tip
 layout: faq
-contributors: [shiltemann,hexylena]
+contributors: [shiltemann,hexylena,nekrut]
 ---
 
-- Click on the {% icon galaxy-pencil %} **pencil icon** for the dataset to edit its attributes
+- Click the desired dataset's name to expand it.
+- Click on the "?" next to database indicator:
+
+  ![UI for changing dbkey]({% link shared/images/datasets_dbkey.svg %})
+
 - In the central panel, change the **Database/Build** field
 - Select your desired database key from the dropdown list{% if include.dbkey %}: `{{ include.dbkey }}`{% endif %}
 - Click the **Save** button

faqs/galaxy/histories_create_new.md

@@ -4,11 +4,12 @@ description: Histories are an important part of Galaxy, most people use a new hi
 area: histories
 box_type: tip
 layout: faq
-contributors: [bebatut,wm75,shiltemann,hexylena,nomadscientist,nsoranzo]
+contributors: [bebatut,wm75,shiltemann,hexylena,nomadscientist,nsoranzo,nekrut]
 ---
 
-Click the {% icon new-history %} icon at the top of the history panel.
+Click the {% icon new-history %} icon at the top of the history panel:
 
-If the {% icon new-history %} is missing:
-1. Click on the {% icon galaxy-gear %} icon (**History options**) on the top of the history panel
-2. Select the option **Create New** from the menu
+![UI for creating new history]({% link shared/images/history_create_new.svg %})
+
+
+<!-- the original drawing can be found here https://docs.google.com/drawings/d/1cCBrLAo4kDGic5QyB70rRiWJAKTenTU8STsKDaLcVU8/edit?usp=sharing -->

faqs/galaxy/histories_list.md

@@ -0,0 +1,35 @@
+---
+title: View a list of all histories
+description: This FAQ demonstrates how to list all histories for a given user
+area: histories
+box_type: tip
+layout: faq
+contributors: [nekrut, hexylena]
+---
+
+There are multiple ways in which you can view your histories:
+
+1. Viewing histories using {% icon switch-histories %} "**Switch to history**" button. This is best for quickly switching between multiple histories.
+
+   Click the "**Switch history**" icon at the top of the history panel to bring up a list of all your histories:
+   ![Listing histories using the "Switch history" button]({% link shared/images/histories_list.svg %})
+
+2. Using the "**Activity Bar**":
+
+   Click the "**Show all histories**" button within the Activity Bar on the left:
+   ![Listing histories using Activity Bar]({% link shared/images/histories_list_via_activity_bar.svg %})
+
+3. Using "**Data**" drop-down:
+
+   Click the "**Data**" link on the top bar of Galaxy interface and select "**Histories**":
+   ![Listing histories using "Data" menu]({% link shared/images/histories_list_via_masthead.svg %})
+
+3. Using the **Multi-view**, which is best for moving datasets between histories:
+
+   Click the {% icon galaxy-history-options %} menu, and select {% icon galaxy-multihistory %} **Show histories side-by-side**
+
+
+
+<!-- Original drawing for histories_list.svg = https://docs.google.com/drawings/d/1fiMTFt4q1DwJllnxjddG0LA-XwKkxyXfPlOqUHteX_k/edit?usp=sharing -->
+<!-- Original drawing for histories_list_via_activity_bar.svg = https://docs.google.com/drawings/d/1YyUMe6hhhejhRaqFEBmG_NwUS_9VXFZY2uYSoUNlFwY/edit?usp=sharing -->
+<!-- Original drawing for histories_list_via_mesthead.svg = https://docs.google.com/drawings/d/1ReFUBwfVlbrKz0pJqY0xxnbb3EjRYJRzoq9bi1NqH-w/edit?usp=sharing -->

faqs/galaxy/histories_sharing.md

@@ -12,7 +12,7 @@ Sharing your history allows others to import and access the datasets, parameters
 Access the history sharing menu via the History Options dropdown ({% icon galaxy-history-options %}), and clicking "{% icon history-share %} Share or Publish"
 
 1. **Share via link**
-   - Open the **History Options** {% icon galaxy-gear %} menu (gear icon) at the top of your history panel and select **Share or Publish**
+   - Open the **History Options** {% icon galaxy-history-options %} menu at the top of your history panel and select "{% icon history-share %} Share or Publish" 
      - {% icon galaxy-toggle %} **Make History accessible**
      - A **Share Link** will appear that you give to others
    - Anybody who has this link can view and copy your history
@@ -31,5 +31,5 @@ Access the history sharing menu via the History Options dropdown ({% icon galaxy
    - Select **Histories shared with me**
    - Here you will see all the histories others have shared with you directly
 
-**Note:** If you want to make changes to your history without affecting the shared version, make a copy by going to {% icon galaxy-gear %} *History options* icon in your history and clicking *Copy*
+**Note:** If you want to make changes to your history without affecting the shared version, make a copy by going to **History Options** {% icon galaxy-history-options %} icon in your history and clicking *Copy this History*
 

faqs/galaxy/histories_side_by_side_view.md

@@ -0,0 +1,20 @@
+---
+title: View histories side-by-side
+description: This FAQ demonstrates how to view histories side-by-sde
+area: histories
+box_type: tip
+layout: faq
+contributors: [nekrut]
+---
+
+You can view multiple Galaxy histories at once. This allows to better understand your analyses and also makes itv possible to drag datasets between histories. This is called "**History multiview**". The multiview can be enabled either view History menu or via the ACtivity Bar:
+
+1. Enabling Multiview via History menu is done by first clicking on the {% icon galaxy-history-options %} "**History options**" drop-down and selecting {% icon galaxy-multihistory %} "**Show Histories Side-by-Side option**":
+
+   ![Enabling side-by-side view using History Options menu]({% link shared/images/histories_side_by_side_view.svg %})
+
+2. Clicking the {% icon galaxy-multihistory %} "**History Multiview**" button within the Activity Bar:
+
+   ![Enabling side-by-side view using Activity Bar]({% link shared/images/histories_multiview_via_activity_bar.svg %})
+
+ <!-- Original drawings are accessible from https://docs.google.com/drawings/d/1coRlf1PxDKZYFt9j83MHGVYvwhBZhBkE-PcnhgIQ6gs/edit?usp=sharing and https://docs.google.com/drawings/d/1ksdR7wf2i5CJA1Pa-frCLMlgfITwwpOh2cKay8xDIi0/edit?usp=sharing -->

faqs/galaxy/reports_collapsible_box.md

@@ -0,0 +1,18 @@
+---
+title: Making an element collapsible in a report
+description: If you have extraneous information you might want to let a user collapse it.
+area: reports
+box_type: tip
+layout: faq
+contributors: [hexylena, guerler]
+---
+
+This applies to any GalaxyMarkdown elements, i.e. the things you've clicked in the left panel to embed in your Workflow Report or Page
+
+By adding a `collapse=""` attribute to a markdown element, you can make it collapsible. Whatever you put in the quotes will be the title of the collapsible box.
+
+````markdown
+```
+history_dataset_type(history_dataset_id=3108c91feeb505da, collapse="[TITLE]")
+```
+````