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Fix test syntax issues. #530

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Fix test syntax issues. #530

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8 changes: 4 additions & 4 deletions ...s/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml
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Expand Up @@ -35,8 +35,8 @@
Database for Busco Lineage: v5
outputs:
Hifiasm HiC hap1:
assert:
has_n_line:
asserts:
has_n_lines:
n: 168
Estimated Genome size: 2288021
Busco Summary Hap1:
Expand All @@ -49,8 +49,8 @@
value: 65000
delta: 10000
usable hap1 gfa:
assert:
has_n_line:
asserts:
has_n_lines:
n: 173
Assembly statistics for Hap1 and Hap2:
asserts:
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4 changes: 2 additions & 2 deletions workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0-tests.yml
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Expand Up @@ -25,6 +25,6 @@
value: 68000
delta: 5000
mitogenome_genbank:
assert:
has_n_line:
asserts:
has_n_lines:
n: 480
4 changes: 0 additions & 4 deletions workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1-tests.yml
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Expand Up @@ -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
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3 changes: 0 additions & 3 deletions ...ows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2-tests.yml
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Expand Up @@ -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
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34 changes: 17 additions & 17 deletions workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection-tests.yml
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Expand Up @@ -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:
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24 changes: 12 additions & 12 deletions ...lows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation-tests.yml
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Expand Up @@ -8,51 +8,51 @@
Select a AMRFinderPlus database: amrfinderplus_V3.12_2024-05-02.2
outputs:
integronfinder2_logfile_text:
assert:
asserts:
has_text:
text: "Writing out results for replicon"
integronfinder2_summary:
assert:
asserts:
has_n_columns:
n: 6
integronfinder2_results_tabular:
assert:
asserts:
has_n_columns:
n: 14
bakta_hypothetical_tabular:
assert:
asserts:
has_n_columns:
n: 9
bakta_annotation_json:
assert:
asserts:
has_text:
text: "aa_hexdigest"
bakta_annotation_tabular:
assert:
asserts:
has_n_columns:
n: 9
isescan_results_tabular:
assert:
asserts:
has_n_columns:
n: 24
isescan_summary_tabular:
assert:
asserts:
has_text:
text: "nIS"
isescan_logfile_text:
assert:
asserts:
has_text:
text: "Both complete and partial IS elements are reported."
plasmidfinder_result_json:
assert:
asserts:
has_text:
text: "positions_in_contig"
plasmidfinder_results_tabular:
assert:
asserts:
has_n_columns:
n: 8
tooldistillator_summarize:
assert:
asserts:
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below there are multiple 'has_text' and only the last one will be tested, right?

has_text:
text: "CDS12738(DOp1)"
has_text:
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15 changes: 8 additions & 7 deletions ...ational-chemistry/fragment-based-docking-scoring/fragment-based-docking-scoring-tests.yml
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Expand Up @@ -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
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I think this will only test the last one, do you have a check for this?

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I don't think that's really checkable as that's a yaml language issue, we don't go that deep.

Comment on lines +24 to +31
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Suggested change
asserts:
has_line:
line: "$$$$"
n: 4
asserts:
has_text:
text: "SuCOS_Score"
n: 4
asserts:
has_line:
line: "$$$$"
n: 4
has_text:
text: "SuCOS_Score"
n: 4

25 changes: 14 additions & 11 deletions workflows/computational-chemistry/gromacs-dctmd/gromacs-dctmd-tests.yml
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Expand Up @@ -21,16 +21,19 @@
XTC files:
element_tests:
split_file_000000.txt:
assert:
has_size: 138900
delta: 500
asserts:
has_size:
size: 138900
delta: 500
Free energy data:
class: 'File'
assert:
has_n_lines: 101
has_n_columns: 5
asserts:
has_n_lines:
n: 101
has_n_columns:
n: 5
Friction data:
class: 'File'
assert:
has_n_lines: 101
has_n_columns: 5
asserts:
has_n_lines:
n: 101
has_n_columns:
n: 5
21 changes: 12 additions & 9 deletions workflows/computational-chemistry/gromacs-mmgbsa/gromacs-mmgbsa-tests.yml
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Expand Up @@ -15,18 +15,21 @@
Salt concentration: 0.1
outputs:
MMGBSA free energy:
class: 'File'
assert:
has_n_lines: 2
asserts:
has_n_lines:
n: 2
MMGBSA statistics:
element_tests:
split_file_000000.txt:
assert:
has_text: 'DELTA TOTAL'
has_text: 'Generalized Born ESURF calculated using LCPO'
asserts:
- that: has_text
text: 'DELTA TOTAL'
- that: has_text
text: 'Generalized Born ESURF calculated using LCPO'
XTC files:
element_tests:
split_file_000000.txt:
assert:
has_size: 138900
delta: 500
asserts:
has_size:
size: 138900
delta: 500
4 changes: 2 additions & 2 deletions ...epigenetics/average-bigwig-between-replicates/average-bigwig-between-replicates-tests.yml
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Expand Up @@ -23,8 +23,8 @@
bin_size: 50
outputs:
average_bigwigs:
class: Collection
collection_type: list
attributes:
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What's the model behind this ? attributes seems kind of odd, shouldn't this nest directly under the output ?

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It should and I will implement that in follow ups but that is an enhancement - this version of the models just reflects what actually works with current planemo. I don't think anyone ever thought this through and so it is a pretty low-level mapping to the XML parsing outputs.

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Don't ask my why I put this test... I cannot remember.

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(I think I am the only one to use this type of test)

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galaxyproject/galaxy#18889

collection_type: list
element_tests:
ATAC_HH19_PT:
asserts:
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20 changes: 12 additions & 8 deletions workflows/epigenetics/cutandrun/cutandrun-tests.yml
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Expand Up @@ -46,13 +46,15 @@
MACS2 summits:
element_tests:
Rep1:
has_n_lines:
n: 1856
asserts:
has_n_lines:
n: 1856
MACS2 narrowPeak:
element_tests:
Rep1:
has_n_lines:
n: 1856
asserts:
has_n_lines:
n: 1856
MACS2 peaks xls:
element_tests:
Rep1:
Expand Down Expand Up @@ -109,13 +111,15 @@
MACS2 summits:
element_tests:
Rep1:
has_n_lines:
n: 3261
asserts:
has_n_lines:
n: 3261
MACS2 narrowPeak:
element_tests:
Rep1:
has_n_lines:
n: 3261
asserts:
has_n_lines:
n: 3261
MACS2 peaks xls:
element_tests:
Rep1:
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1 change: 0 additions & 1 deletion workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler-tests.yml
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Expand Up @@ -81,7 +81,6 @@
value: 47830
delta: 4000
plot with pyGenomeTracks:
class: File
file: test-data/plot_chic.png
compare: sim_size
delta: 1500
1 change: 0 additions & 1 deletion workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml
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Expand Up @@ -79,7 +79,6 @@
value: 149349
delta: 10000
plot with pyGenomeTracks:
class: File
file: test-data/plot_hic.png
compare: sim_size
delta: 1500
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