Edit data import instructions

  - Add new images

Author: vinisalazar

topics/microbiome/tutorials/metagenomics-assembly/images/data-import-1.png

@@ -5,10 +5,10 @@ title: "Assembly of metagenomic sequencing data"
 zenodo_link: "https://zenodo.org/record/7818827"
 level: Introductory
 questions:
-  - "Why metagenomic data should be assembled?"
+  - "Why should metagenomic data be assembled?"
   - "What is the difference between co-assembly and individual assembly?"
   - "What is the difference between reads, contigs and scaffolds?"
-  - "How tools based on De Bruijn graph work?"
+  - "How tools based on de Bruijn graph work?"
   - "How to assess the quality of metagenomic data assembly?"
 objectives:
   - "Describe what an assembly is"
@@ -23,7 +23,7 @@ objectives:
 time_estimation: "2H"
 key_points:
   - "Assembly groups reads into contigs and scafolds."
-  - "De Brujin Graphs use k-mers to assembly reads"
+  - "de Brujin Graphs use k-mers to assembly reads"
   - "MetaSPAdes and MEGAHIT are assemblers"
   - "Quast is the tool to assess the assembly quality"
 edam_ontology:
@@ -33,6 +33,7 @@ contributions:
   authorship:
     - plushz
     - bebatut
+    - vinisalazar
   funding:
     - gallantries
 subtopic: metagenomics
@@ -124,30 +125,39 @@ In case of a not very large dataset it's more convenient to upload data directly
 
 > <hands-on-title>Upload data into Galaxy</hands-on-title>
 >
-> 2. Import the sequence read raw data (\*.fastqsanger.gz) from [Zenodo]({{ page.zenodo_link }}) or a data library:
+> 2. The information we need to import the samples for this tutorial (Sample ID, and link to the FASTQ file (URL) are in the grey box below.
 >
 >    ```text
->    {{ page.zenodo_link }}/files/ERR2231567_1.fastqsanger.gz
->    {{ page.zenodo_link }}/files/ERR2231567_2.fastqsanger.gz
->    {{ page.zenodo_link }}/files/ERR2231568_1.fastqsanger.gz
->    {{ page.zenodo_link }}/files/ERR2231568_2.fastqsanger.gz
->    {{ page.zenodo_link }}/files/ERR2231569_1.fastqsanger.gz
->    {{ page.zenodo_link }}/files/ERR2231569_2.fastqsanger.gz
->    {{ page.zenodo_link }}/files/ERR2231570_1.fastqsanger.gz
->    {{ page.zenodo_link }}/files/ERR2231570_2.fastqsanger.gz
->    {{ page.zenodo_link }}/files/ERR2231571_1.fastqsanger.gz
->    {{ page.zenodo_link }}/files/ERR2231571_2.fastqsanger.gz
->    {{ page.zenodo_link }}/files/ERR2231572_1.fastqsanger.gz
->    {{ page.zenodo_link }}/files/ERR2231572_2.fastqsanger.gz
+>    SampleID URL
+>    ERR2231567_1 {{ page.zenodo_link }}/files/ERR2231567_1.fastqsanger.gz
+>    ERR2231567_2 {{ page.zenodo_link }}/files/ERR2231567_2.fastqsanger.gz
+>    ERR2231568_1 {{ page.zenodo_link }}/files/ERR2231568_1.fastqsanger.gz
+>    ERR2231568_2 {{ page.zenodo_link }}/files/ERR2231568_2.fastqsanger.gz
+>    ERR2231569_1 {{ page.zenodo_link }}/files/ERR2231569_1.fastqsanger.gz
+>    ERR2231569_2 {{ page.zenodo_link }}/files/ERR2231569_2.fastqsanger.gz
+>    ERR2231570_1 {{ page.zenodo_link }}/files/ERR2231570_1.fastqsanger.gz
+>    ERR2231570_2 {{ page.zenodo_link }}/files/ERR2231570_2.fastqsanger.gz
+>    ERR2231571_1 {{ page.zenodo_link }}/files/ERR2231571_1.fastqsanger.gz
+>    ERR2231571_2 {{ page.zenodo_link }}/files/ERR2231571_2.fastqsanger.gz
+>    ERR2231572_1 {{ page.zenodo_link }}/files/ERR2231572_1.fastqsanger.gz
+>    ERR2231572_2 {{ page.zenodo_link }}/files/ERR2231572_2.fastqsanger.gz
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
 >
->    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
+> Import the files from Zenodo using Galaxy's Rule-based Uploader.
+>    - Open the Galaxy Upload Manager
+>    - Click the tab **Rule-based**
+>    - Paste the table.
+>    - Remove the first line.
+>    - Click **Build**
+>    ![Rule-based Uploader](./images/data-import-1.png "Rule-based Uploader")
+>    - On the "Rules" pane on the left, click on "Click here" to set column definitions.
+>    ![Column definitions](./images/data-import-2.png "Column definitions")
+>    - Set the first column as "Name" and the second column as "URL".
+>    ![Upload the data](./images/data-import-3.png "Upload the data")
+>    - Click "Apply" and then "Upload".
 >
->    > <comment-title></comment-title>
->    > In case of large dataset, we can use FTP server or the [Galaxy Rule-based Uploader]({% link topics/galaxy-interface/tutorials/upload-rules/tutorial.md %}).
->    {: .comment}
 >
 > 3. Create a paired collection named `Raw reads`, rename your pairs with the sample name
 >