fix snippet spacing

topics/assembly/tutorials/assembly-with-preprocessing/tutorial.md

@@ -127,6 +127,7 @@ steps are independent of the data source you choose.
 > 1. Create a new history for this tutorial and give it a proper name
 >
 >    {% snippet faqs/galaxy/histories_create_new.md %}
+>
 >    {% snippet faqs/galaxy/histories_rename.md %}
 >
 > 2. Create a new dataset listing the SRA accession numbers of the Illumina paired-end input data for this tutorial:
@@ -220,6 +221,7 @@ steps are independent of the data source you choose.
 > 1. Create a new history for this tutorial and give it a proper name
 >
 >    {% snippet faqs/galaxy/histories_create_new.md %}
+>
 >    {% snippet faqs/galaxy/histories_rename.md %}
 >
 > 2. Import Illumina-sequenced reads data from [Zenodo](https://zenodo.org/record/3732359)

topics/assembly/tutorials/chloroplast-assembly/tutorial.md

@@ -51,6 +51,7 @@ Let's start with uploading the data.
 > 1. Create a new history for this tutorial and give it a proper name
 >
 >    {% snippet faqs/galaxy/histories_create_new.md %}
+>
 >    {% snippet faqs/galaxy/histories_rename.md %}
 >
 > 2. Import from [Zenodo](https://zenodo.org/record/3567224) or a data library (ask your instructor):
@@ -63,6 +64,7 @@ Let's start with uploading the data.
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 {: .hands_on}
 

topics/assembly/tutorials/largegenome/tutorial.md

@@ -126,6 +126,7 @@ We are also using a reference genome *Arabidopsis thaliana* for a later comparis
 > 1. Create a new history for this tutorial and give it a proper name
 >
 >    {% snippet faqs/galaxy/histories_create_new.md %}
+>
 >    {% snippet faqs/galaxy/histories_rename.md %}
 >
 > 2. Import from [Zenodo](https://zenodo.org/record/7055935) or a data library (ask your instructor):
@@ -142,6 +143,7 @@ We are also using a reference genome *Arabidopsis thaliana* for a later comparis
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >    
 > 3. Check that the datatypes for the three files of sequencing reads are `fastq.gz`, not `fastqsanger.gz` and change datatype if needed.

topics/assembly/tutorials/unicycler-assembly/tutorial.md

@@ -164,6 +164,7 @@ In this example we will use a downsampled version of *E. coli* C-1 Illumina and
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 {: .hands_on}

topics/computational-chemistry/tutorials/md-simulation-namd/tutorial.md

@@ -89,6 +89,7 @@ This tool will:
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 > 3. Rename the datasets.

topics/computational-chemistry/tutorials/setting-up-molecular-systems/tutorial.md

@@ -107,6 +107,7 @@ The 7CEL [PDB](https://files.rcsb.org/download/7CEL.pdb) does not include a comp
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 > 3. Rename the datasets.

topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.md

@@ -115,6 +115,7 @@ This first step consist of downloading and properly prepare the data to use it i
 >    for you to find it again later if needed.
 >
 >    {% snippet faqs/galaxy/histories_create_new.md %}
+>
 >    {% snippet faqs/galaxy/histories_rename.md %}
 >
 > 2. Import the CSV files from [Zenodo](https://doi.org/10.5281/zenodo.4264936) via link with the three following links

topics/ecology/tutorials/genetic-map-rad-seq/tutorial.md

@@ -53,6 +53,7 @@ The original data is available at [STACKS website](http://catchenlab.life.illino
 > 1. Create a new history for this RAD-seq exercise.
 >
 >    {% snippet faqs/galaxy/histories_create_new.md %}
+>
 >    {% snippet faqs/galaxy/histories_rename.md %}
 >
 > 2. Import Fasta files from parents and 20 progeny.

topics/ecology/tutorials/species-distribution-modeling/tutorial.md

@@ -51,6 +51,7 @@ In this study the datasets are all imported from the [GBIF](https://www.gbif.org
 > 1. Create a new history for this tutorial and give it a proper name
 >
 >    {% snippet faqs/galaxy/histories_create_new.md %}
+>
 >    {% snippet faqs/galaxy/histories_rename.md %}
 >
 > 2. **Get species occurrences data** {% icon tool %} with the following parameters

topics/epigenetics/tutorials/atac-seq/tutorial.md

@@ -73,6 +73,7 @@ We first need to download the sequenced reads (FASTQs) as well as other annotati
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 > 3. Add a tag called `#SRR891268_R1` to the R1 file and a tag called `#SRR891268_R2` to the R2 file.

topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.md

@@ -95,6 +95,7 @@ To save time, we will do it only on the data of one sample `wt_H3K4me3_rep1` whi
 > 1. Create a new history for this tutorial and give it a proper name
 >
 >    {% snippet faqs/galaxy/histories_create_new.md %}
+>
 >    {% snippet faqs/galaxy/histories_rename.md %}
 >
 > 2. Import `wt_H3K4me3_read1.fastq.gz` and `wt_H3K4me3_read2.fastq.gz` from [Zenodo](https://zenodo.org/record/1324070) or from the data library (ask your instructor)
@@ -105,6 +106,7 @@ To save time, we will do it only on the data of one sample `wt_H3K4me3_rep1` whi
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 >    As default, Galaxy takes the link as name, so rename them.

topics/galaxy-interface/tutorials/intermine/tutorial.md

@@ -78,6 +78,7 @@ You have now exported your query results from InterMine to Galaxy.
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 > 2. Rename the dataset to `GenesLocatedOnChromosome4`

topics/genome-annotation/tutorials/annotation-with-maker/content.md

@@ -85,6 +85,7 @@ To annotate a genome using Maker, you need the following files:
 >    {% endif %}
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 > 3. Rename the datasets

topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.md

@@ -57,6 +57,7 @@ Prokka requires assembled contigs.
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 {: .hands_on}

topics/genome-annotation/tutorials/apollo-euk/tutorial.md

@@ -114,6 +114,7 @@ In this tutorial we use the same data as in the [Funannotate](../funannotate/tut
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 {: .hands_on}

topics/genome-annotation/tutorials/apollo/tutorial.md

@@ -94,6 +94,7 @@ In this tutorial we have obtained some data from NCBI related to [*Escherichia c
 > 0. Create a new history and give it a good name
 >
 >    {% snippet faqs/galaxy/histories_create_new.md %}
+>
 >    {% snippet faqs/galaxy/histories_rename.md %}
 >
 > 1. Click the upload icon {% icon galaxy-upload %}

topics/genome-annotation/tutorials/funannotate/tutorial.md

@@ -104,6 +104,7 @@ To annotate our genome using Funannotate, we will use the following files:
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 {: .hands_on}

topics/genome-annotation/tutorials/functional/tutorial.md

@@ -60,6 +60,7 @@ We will annotate a small set of **protein sequences**. These sequences were pred
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 {: .hands_on}

topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.md

@@ -67,6 +67,7 @@ First we will be uploading the data to Galaxy so that we can run our tools on it
 > 1. Create a new history for this tutorial and give it a descriptive name (e.g. "Mycoplasma comparison hands-on")
 >
 >    {% snippet faqs/galaxy/histories_create_new.md %}
+>
 >    {% snippet faqs/galaxy/histories_rename.md %}
 >
 > 2. Import `mycoplasma-232.fasta` and `mycoplasma-7422.fasta` from [Zenodo](https://zenodo.org/record/4485547#.YBj8XHmCGUk).
@@ -83,6 +84,7 @@ First we will be uploading the data to Galaxy so that we can run our tools on it
 > 3. Rename the files to `232.fasta` and `7422.fasta` and change the datatype if needed to `fasta` (Galaxy will auto-discover the format of the files).
 >
 >    {% snippet faqs/galaxy/datasets_rename.md %}
+>
 >    {% snippet faqs/galaxy/datasets_change_datatype.md %}
 >
 {: .hands_on}
@@ -170,6 +172,7 @@ Let's extract the repeats highlighted in red (Figure 1, right) which are aligned
 > 2. Change the name of the output file `Text reformatting on data ...` to `repeats` Change the datatype to `.fasta`.
 >
 >    {% snippet faqs/galaxy/datasets_rename.md %}
+>
 >    {% snippet faqs/galaxy/datasets_change_datatype.md %}
 >
 > 3. {% tool [ClustalW](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2) %} with the following parameters
@@ -259,6 +262,7 @@ Let us now jump into the hands-on! We will learn how to compare chromosomes with
 > 1. Create a new history for this tutorial and give it a descriptive name (e.g. "Chromosome comparison hands-on")
 >
 >    {% snippet faqs/galaxy/histories_create_new.md %}
+>
 >    {% snippet faqs/galaxy/histories_rename.md %}
 >
 > 2. Import `aegilops_tauschii_chr1.fasta` and `triticum_aestivum_chr1.fasta` from [Zenodo](https://zenodo.org/record/4485547#.YBj8XHmCGUk).
@@ -275,7 +279,9 @@ Let us now jump into the hands-on! We will learn how to compare chromosomes with
 > 3. Rename the files to `aegilops.fasta` and `triticum.fasta` and change the datatype to `fasta` if needed.
 >
 >    {% snippet faqs/galaxy/datasets_rename.md %}
+>
 >    {% snippet faqs/galaxy/datasets_change_datatype.md %}
+>
 >    > <comment-title>Note on the name of the chromosomes</comment-title>
 >    > Please notice that these chromosomes are not labelled as "chromosome 1" at their original sources. We have renamed them for simplicity.
 >    {: .comment}

topics/genome-annotation/tutorials/lncrna/tutorial.md

@@ -99,6 +99,7 @@ To assemble transcriptome with StringTie and annotate {lncRNAs} with FEELnc, we
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 {: .hands_on}

topics/imaging/tutorials/imaging-introduction/tutorial.md

@@ -70,6 +70,7 @@ Our objective is to automatically count the number of cells contained in this im
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 > 3. **Unzip file** {% icon tool %} with the following parameters:

topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.md

@@ -121,6 +121,7 @@ In other words, using a workflow makes it possible to apply the same procedure t
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 >
@@ -136,6 +137,7 @@ In other words, using a workflow makes it possible to apply the same procedure t
 >      - Option 2: Datatypes can be **manually set**
 >
 >    {% snippet faqs/galaxy/datasets_detect_datatype.md datatype="datatypes" %}
+>
 >    {% snippet faqs/galaxy/datasets_change_datatype.md datatype="csv" %}
 >
 > 4. Add an `#iris` tag {% icon galaxy-tags %} to the dataset
@@ -634,6 +636,7 @@ Now that we have built our workflow, let's use it on some different data. For ex
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 > 3. **Rename** {% icon galaxy-pencil %} the dataset to `diamonds`

topics/introduction/tutorials/galaxy-reproduce/tutorial.md

@@ -113,6 +113,7 @@ Each analysis in Galaxy starts by creating a new analysis history and loading da
 >      - Option 2: Datatypes can be **manually set**
 >
 >    {% snippet faqs/galaxy/datasets_detect_datatype.md datatype="datatypes" %}
+>
 >    {% snippet faqs/galaxy/datasets_change_datatype.md datatype="csv" %}
 >
 > 4. Add an `#iris` tag {% icon galaxy-tags %} to the dataset

topics/metagenomics/tutorials/metagenomics-assembly/tutorial.md

@@ -122,6 +122,7 @@ In case of a not very large dataset it's more convenient to upload data directly
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 >    > <comment-title></comment-title>

topics/metagenomics/tutorials/nanopore-16S-metagenomics/tutorial.md

@@ -99,6 +99,7 @@ In this example, we will use a dataset originally hosted in the __NCBI SRA datab
 >     - Assign a name to the new collection: `soil collection`
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 >

topics/metagenomics/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md

@@ -103,6 +103,7 @@ Before we can begin any Galaxy analysis, we need to upload the input data: FASTQ
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 > 2. Add a tag to each dataset (one with `#Barcode10` and the other `#Barcode11`)

topics/metagenomics/tutorials/taxonomic-profiling/tutorial.md

@@ -129,6 +129,7 @@ Now, we need to import the data
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 > 2. Create a paired collection.

topics/proteomics/tutorials/encyclopedia/tutorial.md

@@ -99,6 +99,7 @@ In a typical the DIA-MS experiment, the precursor scan usually ranges between 40
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 > 3. For all the datasets that you have just uploaded, please rename them as follows:

topics/proteomics/tutorials/metaproteomics/tutorial.md

@@ -64,6 +64,7 @@ In this tutorial, we will get the data from Zenodo: [![DOI](https://zenodo.org/b
 > 1. Create a new history and name it something meaningful (e.g. *Metaproteomics tutorial*)
 >
 >    {% snippet faqs/galaxy/histories_create_new.md %}
+>
 >    {% snippet faqs/galaxy/histories_rename.md %}
 >
 > 2. Import the three MGF MS/MS files and the FASTA sequence file from Zenodo.

topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md

@@ -80,6 +80,7 @@ The first step in a tutorial is to get the data from the zenodo link provided an
 > 1. Create a new history for this tutorial and give it a meaningful name
 >
 >    {% snippet faqs/galaxy/histories_create_new.md %}
+>
 >    {% snippet faqs/galaxy/histories_rename.md %}
 >
 > 2. Import the files: 6 MZML files, a Protein FASTA file, and an Experimental Design file from [Zenodo]({{ page.zenodo_link }})
@@ -93,7 +94,9 @@ The first step in a tutorial is to get the data from the zenodo link provided an
 >    https://zenodo.org/record/4037137/files/T7A_1.mzml
 >    https://zenodo.org/record/4037137/files/T7B_1.mzml
 >    ```
+>
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 >

topics/proteomics/tutorials/metaquantome-function/tutorial.md

@@ -74,6 +74,7 @@ The first step in this tutorial is to get the data from the Zenodo link provided
 > 1. Create a new history for this tutorial and give it a meaningful name
 >
 >    {% snippet faqs/galaxy/histories_create_new.md %}
+>
 >    {% snippet faqs/galaxy/histories_rename.md %}
 >
 > 2. Import the files from [Zenodo]({{ page.zenodo_link }}): a Functional File and an Intensity file.

topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.md

@@ -72,6 +72,7 @@ The first step in this tutorial is to get the data from the Zenodo link provided
 > 1. Create a new history for this tutorial and give it a meaningful name.
 >
 >    {% snippet faqs/galaxy/histories_create_new.md %}
+>
 >    {% snippet faqs/galaxy/histories_rename.md %}
 >
 > 2. Import the files from [Zenodo]({{ page.zenodo_link }}): a Functional File and an Intensity file.

topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/tutorial.md

@@ -75,6 +75,7 @@ A high-quality dataset was retrieved from a previously published work {% cite ha
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 > 3. Rename the datasets to their basename (ACPs.fasta, non_ACPs.fasta)

topics/proteomics/tutorials/protein-quant-sil/tutorial.md

@@ -94,6 +94,7 @@ A common problem in mass spectrometry are misassigned mono-isotopic precursor pe
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 >    > <comment-title></comment-title>

topics/sequence-analysis/tutorials/human-reads-removal/tutorial.md

@@ -71,6 +71,7 @@ As always, it is best to give each analysis you are performing with Galaxy its o
 > 1. Create a new history for this tutorial and give it a proper name
 >
 >    {% snippet faqs/galaxy/histories_create_new.md %}
+>
 >    {% snippet faqs/galaxy/histories_rename.md %}
 >
 {: .hands_on}

topics/sequence-analysis/tutorials/mapping/tutorial.md

@@ -65,6 +65,7 @@ In the following, we will process a dataset with the mapper **Bowtie2** and we w
 > 1. Create a new history for this tutorial and give it a proper name
 >
 >    {% snippet faqs/galaxy/histories_create_new.md %}
+>
 >    {% snippet faqs/galaxy/histories_rename.md %}
 >
 > 2. Import `wt_H3K4me3_read1.fastq.gz` and `wt_H3K4me3_read2.fastq.gz` from [Zenodo](https://zenodo.org/record/1324070) or from the data library (ask your instructor)
@@ -75,6 +76,7 @@ In the following, we will process a dataset with the mapper **Bowtie2** and we w
 >    ```
 >
 >    {% snippet faqs/galaxy/datasets_import_via_link.md %}
+>
 >    {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
 >
 >    As default, Galaxy takes the link as name, so rename them.

topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.md

@@ -45,6 +45,7 @@ MAdLandDB is a protein database comprising of a comprehensive collection of full
 > 1. Create a new history for this tutorial and give it a proper name
 >
 >    {% snippet faqs/galaxy/histories_create_new.md %}
+>
 >    {% snippet faqs/galaxy/histories_rename.md %}
 >
 > 2. Import the file `query.faa` from [Zenodo](https://doi.org/10.5281/zenodo.7524427)