Fix galaxy tests

.github/workflows/test.yml

@@ -1,5 +1,7 @@
 name: Test
 on: [push, pull_request]
+env:
+  GALAXY_BRANCH: release_22.05
 jobs:
   build-linux:
     name: Test on Linux
@@ -35,8 +37,8 @@ jobs:
 
         source activate foo
         nosetests --with-doctest -sv deeptools
-  planemo:
-    name: First planemo chunk
+  planemo_test:
+    name: Planemo test
     runs-on: ubuntu-latest
     needs: build-linux
     strategy:
@@ -48,4 +50,45 @@ jobs:
     - name: planemo
       run: |
         source activate foo
-        ./.planemo.sh ${{ matrix.chunk }}
+        conda update -c conda-forge -c bioconda samtools
+        ./.planemo.sh ${{ matrix.chunk }} ${{ env.GALAXY_BRANCH }}
+    - uses: actions/upload-artifact@v3
+      with:
+        name: 'Tool test output ${{ matrix.chunk }}'
+        path: upload
+
+  planemo_combine_outputs:
+    name: Combine chunked test results
+    needs: [build-linux, planemo_test]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.7']
+    steps:
+    - uses: actions/download-artifact@v3
+      with:
+        path: artifacts
+    - uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip
+      uses: actions/cache@v3
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ env.GALAXY_BRANCH }}
+    - name: Combine outputs
+      uses: galaxyproject/planemo-ci-action@v1
+      id: combine
+      with:
+        mode: combine
+        html-report: true
+    - uses: actions/upload-artifact@v3
+      with:
+        name: 'All tool test results'
+        path: upload
+    - name: Check outputs
+      uses: galaxyproject/planemo-ci-action@v1
+      id: check
+      with:
+        mode: check

.planemo.sh

@@ -29,5 +29,6 @@ else
 fi
 
 planemo lint ${wrappers}
-planemo test --no_dependency_resolution --galaxy_branch release_20.09 --install_galaxy ${wrappers} 2>&1 | grep -v -e "^galaxy" | grep -v -e "^requests"
-test ${PIPESTATUS[0]} -eq 0
+planemo test --no_dependency_resolution --galaxy_branch $2 --install_galaxy ${wrappers} 2>&1
+mkdir upload
+mv tool_test_output* upload/

galaxy/wrapper/alignmentSieve.xml

@@ -136,7 +136,7 @@
             <param name="bamfile" value="paired_chr2L.bam" ftype="bam" />
             <param name="minMappingQuality" value="10" />
             <param name="filterMetrics" value="True" />
-            <output name="outFile" file="alignmentSieve.bam" ftype="bam" />
+            <output name="outFile" file="alignmentSieve.bam" ftype="bam" lines_diff="1" />
             <output name="filterMetricsFile" file="alignmentSieve.txt" ftype="tabular" />
         </test>
         <test>
@@ -150,13 +150,13 @@
             <param name="bamfile" value="paired_chr2L.bam" ftype="bam" />
             <param name="minMappingQuality" value="10" />
             <param name="shift" value="1 -2 3 -4" />
-            <output name="outFile" file="alignmentSieve2.bam" ftype="bam" />
+            <output name="outFile" file="alignmentSieve2.bam" ftype="bam" lines_diff="2" />
         </test>
         <test>
             <param name="bamfile" value="paired_chr2L.cram" ftype="cram" />
             <param name="minMappingQuality" value="10" />
             <param name="shift" value="1 -2 3 -4" />
-            <output name="outFile" file="alignmentSieve3.bam" ftype="bam" />
+            <output name="outFile" file="alignmentSieve3.bam" ftype="bam" lines_diff="2" />
         </test>
     </tests>
 

galaxy/wrapper/plotPCA.xml

@@ -78,7 +78,7 @@
             <param name="outFileFormat" value="png" />
             <param name="outFileNameData" value="True" />
             <output name="outFileName" file="plotPCA_result2.png" ftype="png" compare="sim_size" delta="12000" />
-            <output name="output_outFileNameData" file="plotPCA_result2.tabular" ftype="tabular" />
+            <output name="output_outFileNameData" file="plotPCA_result2.tabular" ftype="tabular" lines_diff="2" />
         </test>
     </tests>
     <help>