Add PHI toolkit

workflows/virology/phi-toolkit/.dockstore.yml

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+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /PHI-Toolkit.ga
+  testParameterFiles:
+  - /PHI-Toolkit-tests.yml
+  authors:
+  - name: Matthias Bernt
+    orcid: 0000-0003-3763-0797
+  - name: "Felipe Borim Corr\xEAa"
+    orcid: 0000-0003-0031-1565
+  - name: Joao Pedro Saraiva
+    orcid: 0000-0001-8251-1960
+  - name: "Helmholtz-Zentrum f\xFCr Umweltforschung GmbH - UFZ"
+    url: https://www.ufz.de/

workflows/virology/phi-toolkit/CHANGELOG.md

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+# Changelog
+
+## [0.1] - 2025-07-09
+
+Addition of the workflow to the iwc repository.

workflows/virology/phi-toolkit/PHI-Toolkit-tests.yml

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+- doc: Test outline for PHI-Toolkit
+  job:
+    Host contigs:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: NC_021184.fasta
+        location: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_021184&rettype=fasta&retmode=text
+      - class: File
+        identifier: NC_019936.fasta
+        location: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_019936&rettype=fasta&retmode=text
+      - class: File
+        identifier: NC_019904.fasta
+        location: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_019904&rettype=fasta&retmode=text
+      - class: File
+        identifier: NC_019897.fasta
+        location: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_019897&rettype=fasta&retmode=text
+      - class: File
+        identifier: NC_018515.fasta
+        location: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_018515&rettype=fasta&retmode=text
+      - class: File
+        identifier: NC_018068.fasta
+        location: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_018068&rettype=fasta&retmode=text
+      - class: File
+        identifier: NC_018014.fasta
+        location: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_018014&rettype=fasta&retmode=text
+      - class: File
+        identifier: NC_017095.fasta
+        location: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_017095&rettype=fasta&retmode=text
+      - class: File
+        identifier: NC_017033.fasta
+        location: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_017033&rettype=fasta&retmode=text
+      - class: File
+        identifier: NC_015761.fasta
+        location: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_015761&rettype=fasta&retmode=text
+      - class: File
+        identifier: NC_014364.fasta
+        location: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_014364&rettype=fasta&retmode=text
+      - class: File
+        identifier: NC_014363.fasta
+        location: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_014363&rettype=fasta&retmode=text
+      - class: File
+        identifier: NC_014212.fasta
+        location: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_014212&rettype=fasta&retmode=text
+      - class: File
+        identifier: NC_014211.fasta
+        location: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_014211&rettype=fasta&retmode=text
+      - class: File
+        identifier: NC_014168.fasta
+        location: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_014168&rettype=fasta&retmode=text
+      - class: File
+        identifier: NC_014008.fasta
+        location: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_014008&rettype=fasta&retmode=text
+      - class: File
+        identifier: NC_012982.fasta
+        location: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_012982&rettype=fasta&retmode=text
+      - class: File
+        identifier: NC_009012.fasta
+        location: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_009012&rettype=fasta&retmode=text
+      - class: File
+        identifier: NC_008261.fasta
+        location: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_008261&rettype=fasta&retmode=text
+      - class: File
+        identifier: NC_003450.fasta
+        location: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_003450&rettype=fasta&retmode=text
+      - class: File
+        identifier: NC_002737.fasta
+        location: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_002737&rettype=fasta&retmode=text
+      - class: File
+        identifier: NC_000913.fasta
+        location: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_000913&rettype=fasta&retmode=text
+    GTDB-Tk database: Full Database - Release 220 (2024-10-19)
+    Agree with genomad license: true
+  outputs: 
+    PHI toolkit report:
+      asserts:
+        has_text:
+          text: html
+        has_size:
+          size: 100
+        has_text:
+          text: "Error: "
+          negate: true