Merge pull request galaxyproject#372 from debjyoti197/qiime2-part2

QIIME2 downstream workflows

workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml

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+version: 1.2
+workflows:
+- name: QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga
+  testParameterFiles:
+  - /QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml
+  authors:
+  - name: Debjyoti Ghosh
+    orcid: 0009-0008-1496-1677
+  - name: "Helmholtz-Zentrum für Umweltforschung - UFZ"
+    address: "Permoserstraße 15, 04318 Leipzig"
+
+- name: QIIME2-VI-diversity-metrics-and-estimations
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /QIIME2-VI-diversity-metrics-and-estimations.ga
+  testParameterFiles:
+  - /QIIME2-VI-diversity-metrics-and-estimations-tests.yml
+  authors:
+  - name: Debjyoti Ghosh
+    orcid: 0009-0008-1496-1677
+  - name: "Helmholtz-Zentrum für Umweltforschung - UFZ"
+    address: "Permoserstraße 15, 04318 Leipzig"

workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.workflowhub.yml

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+version: '0.1'
+registries:
+- url: https://workflowhub.eu
+  project: iwc
+  workflow: qiime2/main

workflows/amplicon/qiime2/qiime2-III-VI-downsteam/CHANGELOG.md

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+# Changelog
+
+## [0.1] 2024-06-22
+First release.

workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml

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+- doc: Test outline for QIIME2-III:-Phylogenetic-tree-for-diversity-analysis
+  job:
+    Metadata:
+      class: File
+      location: https://data.qiime2.org/2024.2/tutorials/pd-mice/sample_metadata.tsv
+      filetype: tabular
+    Representative sequences:
+      class: File
+      location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/dada2_rep_set.qza
+      filetype: qza
+    Feature table:
+      class: File
+      location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/dada2_table.qza
+      filetype: qza
+    Minimum depth: 1
+    Maximum depth: 2019
+    Taxonomic classifier:
+      class: File
+      location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/gg-13-8-99-515-806-nb-classifier.qza
+      filetype: qza
+    SEPP fragment insertion reference:
+      class: File
+      location: https://data.qiime2.org/2024.2/common/sepp-refs-gg-13-8.qza
+      filetype: qza
+  outputs:
+    Rooted tree:
+      ftype: qza
+      asserts:
+        - has_size:
+            min: 2M
+            max: 3M
+        - has_archive_member:
+            path: "^[^/]*/data/tree.nwk"
+            n: 1
+            asserts:
+              - has_text_matching:
+                  expression: "k__Bacteria"
+        - has_archive_member:
+            path: "^[^/]*/metadata.yaml"
+            n: 1
+            asserts:
+              - has_line:
+                  line: "type: Phylogeny[Rooted]"
+              - has_line:
+                  line: "format: NewickDirectoryFormat"
+
+    Rarefaction curve:
+      ftype: qzv
+      asserts:
+        - has_size:
+            min: 400k
+            max: 500k
+        - has_archive_member:
+            path: "^[^/]*/data/index.html"
+            n: 1
+        # data per measure
+        - has_archive_member:
+            path: "^[^/]*/data/.*\\.csv"
+            n: 3
+        # data for each measure and metadata variable (*7)
+        - has_archive_member:
+            path: "^[^/]*/data/.*\\.jsonp"
+            n: 21
+
+    Taxonomy classification:
+      ftype: qza
+      asserts:
+        - has_size:
+            min: 70k
+            max: 80k
+        - has_archive_member:
+            path: "^[^/]*/metadata.yaml"
+            n: 1
+            asserts:
+              - has_line:
+                  line: "type: FeatureData[Taxonomy]"
+              - has_line:
+                  line: "format: TSVTaxonomyDirectoryFormat"
+        - has_archive_member:
+            path: "^[^/]*/data/taxonomy.tsv"
+            n: 1
+            asserts:
+              - has_n_lines:
+                  n: 288
+    Taxa barplot:
+      ftype: qzv
+      asserts:
+        - has_size:
+            min: 400k
+            max: 500k
+        - has_archive_member:
+            path: "^[^/]*/data/.*\\.csv"
+            n: 7
+        - has_archive_member:
+            path: "^[^/]*/data/.*\\.jsonp"
+            n: 7
+    Taxonomy classification table:
+      ftype: qza
+      asserts:
+        - has_size:
+            min: 1M
+            max: 2M
+        - has_archive_member:
+            path: "^[^/]*/data/metadata.tsv"
+            n: 1
+            asserts:
+              - has_n_lines:
+                  n: 289