Fix test syntax issues passing

galaxyproject · Sep 24, 2024 · fc78f57 · fc78f57
1 parent 7907910
commit fc78f57
Show file tree

Hide file tree

Showing 11 changed files with 50 additions and 64 deletions.
diff --git a/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0-tests.yml b/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0-tests.yml
@@ -25,6 +25,6 @@
           value: 68000
           delta: 5000
     mitogenome_genbank:
-      assert:
-        has_n_line:
+      asserts:
+        has_n_lines:
           n: 480
diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1-tests.yml b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1-tests.yml
@@ -12,22 +12,18 @@
     Ploidy: 1
   outputs:
     GenomeScope linear plot:
-      class: File
       file: test-data/GenomeScope_Linear_plot.png
       compare: sim_size
       delta: 10000
     GenomeScope log plot:
-      class: File
       file: test-data/GenomeScope_Log_plot.png
       compare: sim_size
       delta: 10000
     GenomeScope transformed linear plot:
-      class: File
       file: test-data/GenomeScope_Transformed_linear_plot.png
       compare: sim_size
       delta: 10000
     GenomeScope transformed log plot:
-      class: File
       file: test-data/GenomeScope_Transformed_log_plot.png
       compare: sim_size
       delta: 10000

diff --git a/...ows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2-tests.yml b/...ows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2-tests.yml
@@ -36,17 +36,14 @@
     Ploidy: 1
   outputs:
     GenomeScope linear plot (maternal):
-      class: File
       file: test-data/GenomeScope_Linear_plot_maternal.png
       compare: sim_size
       delta: 15000
     GenomeScope linear plot (paternal):
-      class: File
       file: test-data/GenomeScope_Linear_plot_paternal.png
       compare: sim_size
       delta: 15000
     GenomeScope linear plot (child):
-      class: File
       file: test-data/GenomeScope_Linear_plot_child.png
       compare: sim_size
       delta: 15000

diff --git a/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection-tests.yml b/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection-tests.yml
@@ -5,55 +5,55 @@
       path: https://zenodo.org/records/11488310/files/shovill_contigs_fasta
   outputs:
     staramr_detailed_summary:
-        assert:
-        has_text:
-          text: "Resistance"
-        has_n_columns:
-          n: 12
+        asserts:
+          has_text:
+            text: "Resistance"
+          has_n_columns:
+            n: 12
     staramr_resfinder_report:
-        assert:
-        has_text:
-          text: "tetracycline"
-        has_n_columns:
-          n: 13
+        asserts:
+          has_text:
+            text: "tetracycline"
+          has_n_columns:
+            n: 13
     staramr_mlst_report:
-      assert:
+      asserts:
         has_text:
           text: "efaecalis"
         has_n_columns:
           n: 10
     staramr_plasmidfinder_report:
-      assert:
+      asserts:
         has_text:
           text: "CP002494"
         has_n_columns:
           n: 9
     staramr_summary:
-      assert:
+      asserts:
         has_text:
           text: "streptomycin"
         has_n_columns:
           n: 12
     amrfinderplus_report:
-      assert:
+      asserts:
         has_text:
           text: "Enterococcus faecalis quinolone resistant ParC"
         has_n_columns:
           n: 23
     amrfinderplus_mutation:
-      assert:
+      asserts:
         has_text:
           text: "cardiolipin synthase Cls"
         has_n_columns:
           n: 23
     abricate_virulence_report:
-      assert:
+      asserts:
         has_text:
           text: "endocarditis specific antigen"
         has_n_columns:
           n: 15
     tooldistillator_summarize:
-      assert:
+      asserts:
         has_text:
           text: "% Identity to reference sequence"
         has_text:

diff --git a/...ational-chemistry/fragment-based-docking-scoring/fragment-based-docking-scoring-tests.yml b/...ational-chemistry/fragment-based-docking-scoring/fragment-based-docking-scoring-tests.yml
@@ -21,10 +21,11 @@
     SuCOS threshold: 0
   outputs:
     Scored and filtered poses:
-      class: File
-      assert:
-        has_line: "$$$$"
-        n: 4
-      assert:
-        has_test: "SuCOS_Score"
-        n: 4
+      asserts:
+        has_line:
+          line: "$$$$"
+          n: 4
+      asserts:
+        has_text:
+          text: "SuCOS_Score"
+          n: 4
diff --git a/...epigenetics/average-bigwig-between-replicates/average-bigwig-between-replicates-tests.yml b/...epigenetics/average-bigwig-between-replicates/average-bigwig-between-replicates-tests.yml
@@ -23,8 +23,8 @@
     bin_size: 50
   outputs:
     average_bigwigs:
-      class: Collection
-      collection_type: list
+      attributes:
+        collection_type: list
       element_tests:
         ATAC_HH19_PT:
           asserts:

diff --git a/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler-tests.yml b/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler-tests.yml
@@ -81,7 +81,6 @@
               value: 47830
               delta: 4000
     plot with pyGenomeTracks:
-      class: File
       file: test-data/plot_chic.png
       compare: sim_size
       delta: 1500
diff --git a/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml
@@ -79,7 +79,6 @@
               value: 149349
               delta: 10000
     plot with pyGenomeTracks:
-      class: File
       file: test-data/plot_hic.png
       compare: sim_size
       delta: 1500
diff --git a/...me-assembly/quality-and-contamination-control/quality_and_contamination_control-tests.yml b/...me-assembly/quality-and-contamination-control/quality_and_contamination_control-tests.yml
@@ -12,52 +12,52 @@
     Select a NCBI taxonomy database: "2022-03-08"
   outputs:
     fastp_report_json:
-      assert:
+      asserts:
         has_text:
           text: "fastp_version"
         has_text:
           text: "read2_before_filtering"
     kraken_report_tabular:
-      assert:
+      asserts:
         has_text:
           text: "Enterococcus avium"
-        has_n_column:
+        has_n_columns:
           n: 6
     kraken_report_reads:
-      assert:
+      asserts:
         has_text:
           text: "M07044:90:000000000-JRJWP:1:1119:23974:4461"
-        has_n_column:
+        has_n_columns:
           n: 5
     bracken_kraken_report:
-      assert:
+      asserts:
         has_text:
           text: "Enterococcus gallinarum"
-        has_n_column:
+        has_n_columns:
           n: 6
     bracken_report_tsv:
-      assert:
+      asserts:
         has_text:
           text: "Escherichia coli"
-        has_n_column:
+        has_n_columns:
           n: 7
     recentrifuge_data_tabular:
-      assert:
+      asserts:
         has_text:
           text: "Enterococcus faecalis"
-        has_n_column:
+        has_n_columns:
           n: 6
     recentrifuge_stats_tabular:
-      assert:
+      asserts:
         has_text:
           text: "input_dir/kraken_report_reads"
-        has_n_column:
+        has_n_columns:
           n: 2
     tooldistillator_summarize:
-      assert:
-        has_text:
+      asserts:
+        - that: has_text
           text: "fastp_report"
-        has_text:
+        - that: has_text
           text: "ncbi_taxonomic_id"
-        has_text:
+        - that: has_text
           text: "kraken2_report"
diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml
@@ -54,15 +54,13 @@
     Number of expected cells: 500
   outputs:
     MultiQC_STARsolo:
-      class: File
       asserts:
         - that: "has_text_matching"
           expression: ">subsample</th><td class=\"data-coloured mqc-generalstats-star-uniquely_mapped_percent \"><div class=\"wrapper\"><span class=\"bar\""
         - that: "has_text_matching"
           expression: "></span><span class=\"val\">3[0-9].[0-9]%</span></div></td><td class=\"data-coloured mqc-generalstats-star-uniquely_mapped \"><div class=\"wrapper\"><span class=\"bar\""
     Seurat input for gene expression (filtered):
-      class: Collection
-      collection_type: list:list
+      attributes: { collection_type: list:list }
       element_tests:
         subsample:
           elements:
@@ -79,8 +77,7 @@
                 has_line:
                   line: "FBgn0250732	gfzf"
     CITE-seq-Count report:
-      class: Collection
-      collection_type: list
+      attributes: { collection_type: list }
       element_tests:
         subsample:
           asserts:
@@ -93,8 +90,7 @@
             - that: "has_line"
               line: "Percentage unmapped: 1"
     Seurat input for CMO (UMI):
-      class: Collection
-      collection_type: list:list
+      attributes: { collection_type: list:list }
       element_tests:
         subsample:
           elements:

diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3-tests.yml b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3-tests.yml
@@ -29,15 +29,13 @@
       filetype: tabular
   outputs:
     'MultiQC on input dataset(s): Webpage':
-      class: File
       asserts:
         - that: "has_text_matching"
           expression: ">subsample</th><td class=\"data-coloured mqc-generalstats-star-uniquely_mapped_percent \"><div class=\"wrapper\"><span class=\"bar\""
         - that: "has_text_matching"
           expression: "></span><span class=\"val\">3[0-9].[0-9]%</span></div></td><td class=\"data-coloured mqc-generalstats-star-uniquely_mapped \"><div class=\"wrapper\"><span class=\"bar\""
     Seurat input for gene expression (filtered):
-      class: Collection
-      collection_type: list:list
+      attributes: { collection_type: list:list }
       element_tests:
         subsample:
           elements: