testing cleanup

.github/workflows/ci.yaml

@@ -6,15 +6,15 @@ on:
   repository_dispatch:
     types: [run-all-tool-tests-command]
 env:
-  GALAXY_RELEASE: release_20.09
+  GALAXY_RELEASE: release_24.0
 jobs:
   setup:
     name: Setup cache
     if: github.repository_owner == 'computational-metabolomics'
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7]
+        python-version: [3.11]
     steps:
     - name: Add reaction
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
@@ -52,7 +52,7 @@ jobs:
       fail-fast: false
       matrix:
         chunk: [0,1,2,3]
-        python-version: [3.7]
+        python-version: [3.11]
     services:
       postgres:
         image: postgres:11

.github/workflows/pr.yaml

@@ -2,7 +2,7 @@ name: Galaxy Tool Linting and Tests for push and PR
 on: [push, pull_request]
 env:
   GALAXY_REPO: https://github.com/galaxyproject/galaxy
-  GALAXY_RELEASE: release_20.09
+  GALAXY_RELEASE: release_24.0
 jobs:
   # the setup job does two things:
   # 1. cache the pip cache and .planemo
@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7]
+        python-version: [3.11]
     steps:
     - name: Print github context properties
       run: |
@@ -100,7 +100,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7]
+        python-version: [3.11]
     steps:
     # checkout the repository
     # and use it as the current working directory
@@ -139,7 +139,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7]
+        python-version: [3.11]
     steps:
     # checkout the repository to master
     # and use it as the current working directory
@@ -175,7 +175,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        r-version: [4.0.1]
+        r-version: [4.4.0]
     steps:
     # checkout the repository to master
     # and use it as the current working directory

README.rst

@@ -1,15 +1,15 @@
 msPurity for Galaxy
 ========================
-|Build Status (Travis)| |Git| |Bioconda| |License|
+|Git| |Bioconda| |License|
 
 
-Version v1.16.2+galaxy1
+Version v1.16.2+galaxy2
 ------------------------
 
   - msPurity
      - bioconductor-mspurity v1.16.2
   - Galaxy tools
-     - v1
+     - v2
 
 About
 ------
@@ -54,6 +54,12 @@ Authors, contributors & contacts
 
 Changes
 -------------------------
+v1.16.2-galaxy2 
+  - Fix for purityX galaxy tool (https://github.com/computational-metabolomics/mspurity-galaxy/issues/53) 
+  - Cleanup of xml based on updated lint requirements
+  - Fix combineAnnotation tests
+  - Cleanup of repository folders
+
 v1.16.2-galaxy1
   - Fix for "scan" option for spectral matching
   - Add allfrag option for filterFragSpectra

tools/msPurity/combineAnnotations.xml

@@ -113,9 +113,10 @@
         <test>
             <param name="sm_resultPth" value="combinedAnnotation_input_spectralMatching.sqlite" />
             <param name="metfrag_resultPth" value="combineAnnotations_input_metfrag.tsv" />
-	    <param name="sirius_csi_resultPth" value="combineAnnotations_input_sirus_csifingerid.tsv" />
-             <param name="compoundDbTypeCond|compoundDbPth" value="metab_compound_subset.sqlite" />
+	        <param name="sirius_csi_resultPth" value="combineAnnotations_input_sirus_csifingerid.tsv" />
+            <param name="compoundDbTypeCond|compoundDbPth" value="metab_compound_subset.sqlite" />
             <param name="ms1_lookup_resultPth" value="combineAnnotations_input_beams.tsv" />
+            <param name="ms1_lookup_keepAdducts" value="[M+H]+, [M+Na]+" />
             <param name="compoundDbTypeCond|compoundDbPth" value="metab_compound_subset.sqlite" />
             <output name="combined_annotations_tsv" file="combineAnnotations_combined_annotations.tsv" ftype="tsv" />
             <output name="combined_annotations_sqlite" file="combineAnnotations_combined_annotations.sqlite" ftype="sqlite" compare="sim_size"/>