Dev aina

.gitignore

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+python-3.14.3-amd64 (1).exe
+venv
+venv311
+.DS_Stores
+agrf/base.yml

agrf/sections/gbs.yml

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+id: gbs
+title: GBS
+
+tabs:
+  - id: overview
+    title: Overview
+    content:
+      - title_md: About the service
+        description_md: |
+          Genotyping-by-sequencing (GBS/ddRADSeq) is used to identify genetic variants across multiple samples for population genetics studies.
+
+          AGRF performs primary GBS analysis using NGSEP due to its efficiency for large sample sets. The outputs typically include variant call files (VCF) and consensus sequences (FASTA).
+
+          This Galaxy section supports downstream analysis of these outputs. Users can import VCF files into Galaxy and perform variant filtering, population genetic analysis, and visualisation using tools such as VCFtools and PLINK.
+      - title_md: Results include
+        description_md: |
+          **Raw read data** - Demultiplexed sequencing reads in FASTQ format
+
+          **Variant calls** - VCF files containing SNP and genotype information
+
+          **Consensus sequences** - FASTA files containing consensus sequences
+
+          **Filtered variant outputs** - VCF files filtered by missingness, minor allele frequency, or other criteria
+
+          **PLINK outputs** - Files prepared for downstream population genetic analysis
+
+          **Distance and visualisation outputs** - IBS distance matrix and heatmap-style outputs for sample comparison
+
+      - title_md: What files are included?
+        description_md: |
+          | **Filename** | **Description** |
+          |-------------|----------------|
+          | Demultiplexed *.FASTQ files | Raw sequencing reads for each sample |
+          | variants.vcf | Variant calls containing SNP and genotype information |
+          | consensus_sequences.fasta | Consensus sequences generated from variant/locus analysis |
+          | filtered_high_level.vcf | VCF filtered using stricter missingness and MAF thresholds |
+          | filtered_low_level.vcf | VCF filtered using less stringent missingness and MAF thresholds |
+          | populations.plink.* | PLINK-format files generated from VCF data |
+          | ibs_distance_matrix.tsv | Identity-by-state distance matrix for sample comparison |
+          | heatmap_output.html / .png | Visualisation output showing sample relatedness or clustering |
+
+      - title_md: File formats used
+        description_md: |
+          | **Type** | **Description** |
+          |---------|----------------|
+          | .fastq | Raw sequencing reads |
+          | .vcf | Variant call format containing SNP and genotype data |
+          | .fasta / .fa | Consensus sequences or assembled loci |
+          | .ped / .map | PLINK genotype input files |
+          | .tsv / .txt | Tabular outputs, filtering summaries, or distance matrices |
+          | .html / .png | Visualisation outputs such as heatmaps |
+
+  - id: tools
+    title: Tools
+    content:
+      subsections:
+        - id: stacks
+          title: STACKS workflow
+          content:
+
+            - title_md: <code>ustacks</code> - Build loci for each sample
+              description_md: |
+                Build loci from sequencing reads for each sample.
+              inputs:
+                - label: Sequencing reads (FASTQ)
+                  datatypes:
+                    - fastqsanger
+              outputs:
+                - label: Sample loci
+              button_md: Run ustacks
+              button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks_ustacks%2Fstacks_ustacks"
+
+            - title_md: <code>cstacks</code> - Create catalog of loci
+              description_md: |
+                Create a catalog of loci across multiple samples.
+              inputs:
+                - label: Loci from multiple samples
+                  datatypes:
+                    - tabular
+              outputs:
+                - label: Catalog of loci
+              button_md: Run cstacks
+              button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks_cstacks%2Fstacks_cstacks"
+
+            - title_md: <code>sstacks</code> - Match samples to catalog
+              description_md: |
+                Match each sample to the catalog of loci.
+              inputs:
+                - label: Sample loci
+                  datatypes:
+                    - tabular
+                - label: Catalog of loci
+                  datatypes:
+                    - tabular
+              outputs:
+                - label: Matches to catalog
+              button_md: Run sstacks
+              button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_sstacks%2Fstacks2_sstacks"
+
+            - title_md: <code>tsv2bam</code> - Convert TSV to BAM
+              description_md: |
+                Convert TSV genotype data into BAM format for downstream analysis.
+              inputs:
+                - label: Loci and polymorphism
+                  datatypes:
+                    - tabular
+                - label: Catalog of loci
+                  datatypes:
+                    - tabular
+                - label: Matches to catalog
+                  datatypes:
+                    - tabular
+              outputs:
+                - label: BAM alignments
+              button_md: Run tsv2bam
+              button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_tsv2bam%2Fstacks2_tsv2bam"
+
+            - title_md: <code>gstacks</code> - Assemble loci and call variants
+              description_md: |
+                Assemble loci, align reads, and perform variant calling.
+              inputs:
+                - label: BAM alignments
+                  datatypes:
+                    - bam
+              outputs:
+                - label: Variant calls and assembled loci
+              button_md: Run gstacks
+              button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_gstacks%2Fstacks2_gstacks"
+
+            - title_md: <code>populations</code> - Population genetics analysis
+              description_md: |
+                Generate population-level statistics and export results for downstream analysis.
+              inputs:
+                - label: Variant calls / loci
+                  datatypes:
+                    - vcf
+              outputs:
+                - label: Population statistics and export files
+              button_md: Run populations
+              button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fstacks2_populations%2Fstacks2_populations"
+
+            - title_md: <code>bcftools filter</code> - Filter variant data
+              description_md: Filter variant call files (VCF) based on minor allele frequency (MAF), missing data thresholds, and quality metrics for downstream population analysis.
+              button_md: Launch Tool
+              button_link: "{{ galaxy_base_url }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbcftools_filter%2Fbcftools_filter"
+
+  - id: tutorials
+    title: Tutorials
+    content:
+      - title_md: GBS analysis tutorials
+        description_md: Explore Galaxy Training Network tutorials for variant analysis workflows relevant to GBS and population genomics studies.
+        button_md: Tutorials
+        button_link: https://training.galaxyproject.org/training-material/topics/variant-analysis/

agrf/sections/learn.yml

@@ -1,14 +1,58 @@
 id: learn
 title: Learn Galaxy
+
 tabs:
   - id: overview
     title: Overview
-    heading_md: 
+    heading_md:
+      Learn how to use Galaxy through tutorials, workflows, and official documentation.
     content:
-      - title_md: abc
+      - title_md: Galaxy Training Resources
+        description_md: |
+          Learn how to use Galaxy through step-by-step tutorials from the Galaxy Training Network.
+          These resources cover a wide range of bioinformatics workflows including RNA-seq,
+          microbiome analysis, metagenomics, and variant analysis.
+        button_md: Browse Tutorials
+        button_link: https://training.galaxyproject.org/training-material/
+
+      - title_md: Variant Analysis Tutorials
+        description_md: |
+          Explore tutorials for SNP calling, variant analysis, and related workflows
+          relevant to GBS and population genomics studies.
+        button_md: View Tutorials
+        button_link: https://training.galaxyproject.org/training-material/topics/variant-analysis/
+
+      - title_md: Microbiome Tutorials
+        description_md: |
+          Learn microbial community analysis workflows in Galaxy, including QIIME 2 based
+          approaches for diversity analysis and taxonomic profiling.
+        button_md: View Tutorials
+        button_link: https://training.galaxyproject.org/training-material/topics/microbiome/
+
+      - title_md: RNA-seq Tutorials
+        description_md: |
+          Learn RNA-seq analysis workflows in Galaxy, including alignment, quantification,
+          and differential expression analysis.
+        button_md: View Tutorials
+        button_link: https://training.galaxyproject.org/training-material/topics/transcriptomics/
+
+      - title_md: Metagenomics Tutorials
         description_md: |
-          * abc
+          Explore tutorials for metagenome assembly, classification, and downstream
+          analysis workflows in Galaxy.
+        button_md: View Tutorials
+        button_link: https://training.galaxyproject.org/training-material/topics/metagenomics/
 
-
-        button_md: Upload data
-        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=upload1"
+      - title_md: GBS and Population Genomics Tutorials
+        description_md: |
+          Learn workflows relevant to Genotyping-by-Sequencing (GBS), including variant calling,
+          SNP analysis, and population genomics approaches in Galaxy.
+        button_md: View Tutorials
+        button_link: https://training.galaxyproject.org/training-material/topics/variant-analysis/
+
+      - title_md: Galaxy Help and Documentation
+        description_md: |
+          Access official Galaxy documentation, user guides, and help resources to understand
+          tools, workflows, and data management in Galaxy.
+        button_md: Open Documentation
+        button_link: https://galaxyproject.org/learn/