tests: json should parsing

see #3206

algo/tests/should-get-tests/algo-then-fuse.should

 !REQUIRES: python $VIDJIL_DIR/tools/check_python_version.py
-!LAUNCH: $VIDJIL_DIR/$EXEC -r 1 -z 0 -w 60 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta ; python $VIDJIL_DIR/tools/fuse.py out/Stanford_S22.vidjil out/Stanford_S22.vidjil -o out/fused.data ; cat out/fused.data | python $VIDJIL_DIR/tools/format_json.py -1
+
+!OUTPUT_FILE: out/algo-then-fuse.vidjil
+!OPTIONS: --mod jR
+
+!LAUNCH: $VIDJIL_DIR/$EXEC -r 1 -z 0 -w 60 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta ; python $VIDJIL_DIR/tools/fuse.py out/Stanford_S22.vidjil out/Stanford_S22.vidjil -o out/algo-then-fuse.vidjil
 
 $ Points list
-1:"original_names": \[".*data//Stanford_S22.fasta", ".*data//Stanford_S22.fasta"\]
+2:samples.original_names
+:samples.original_names[0]: data//Stanford_S22.fasta
+:samples.original_names[1]: data//Stanford_S22.fasta
 
 $ Most abundant window, twice, fused
-1:"id": "CCACCTATTACTGTACCCGGGAGGAACAATATAGCAGCTGGTACTTTGACTTCTGGGGCC".*"reads": \[8, 8\].*"top": 2
+:clones[0].id: CCACCTATTACTGTACCCGGGAGGAACAATATAGCAGCTGGTACTTTGACTTCTGGGGCC
+:clones[0].reads: [8, 8]
+:clones[0].top: 1
 
 $ Windows that are not in the bottom of the distribution
-1: "distribution": \{[^}]+ "0.00001": \[9062, 9062\]
+#  :reads.distribution.0.00001:  should#59
+:reads.distribution: [9062, 9062]
\ No newline at end of file

tools/tests/should-get-tests/pear_structured_log.should-get

-!LAUNCH: python ../../pear_structured_log.py -i ../data/pear_log.log -o ../data/pear_strucured.json; cat ../data/pear_strucured.json
+!OUTPUT_FILE: ../data/pear_strucured.json
+!LAUNCH: python ../../pear_structured_log.py -i ../data/pear_log.log -o ../data/pear_strucured.json
 
-$ Correct number of assembled reads
-1:"reads_assembled_number": 2972
+!OPTIONS: --mod jR
 
-1:"reads_total_number": 3000
+$ Correct number of assembled reads
+:reads.reads_assembled_number: 2972
+:reads.reads_total_number: 3000
 
 $ Correct number of unassembled reads
-1:"reads_not_assembled_number": 28
+:reads.reads_not_assembled_number: 28
 
 $ Correct information on input files used by pear
-1:"assembled_reads": "demo_set.fastq.assembled.fastq", 
-1:"discarded_reads": "demo_set.fastq.discarded.fastq", 
-1:"unassembled_forward": "demo_set.fastq.unassembled.forward.fastq", 
-1:"unassembled_reverse": "demo_set.fastq.unassembled.reverse.fastq"
+:output_file.assembled_reads: demo_set.fastq.assembled.fastq
+:output_file.discarded_reads: demo_set.fastq.discarded.fastq
+:output_file.unassembled_forward: demo_set.fastq.unassembled.forward.fastq
+:output_file.unassembled_reverse: demo_set.fastq.unassembled.reverse.fastq
 
 $ Correct parameter return
-1:"forward_file": "sequence_R1.fastq", 
-1:"minimum_overlap": "10", 
-1:"phred": "33", 
-1:"reverse_file": "sequence_R2.fastq", 
-1:"scoring_methode": "Scaled score", 
-1:"version": "PEAR v0.9.10 \[May 30, 2016\]"
-
+:settings.forward_file: sequence_R1.fastq
+:settings.minimum_overlap: 10
+:settings.phred: 33
+:settings.reverse_file: sequence_R2.fastq
+:settings.scoring_methode: Scaled score
+:settings.version: PEAR v0.9.10 \[May 30, 2016\]
 
 $ Correct nucleotides frequencies
-1:"base_frequency_a": "0.269874", 
-1:"base_frequency_c": "0.257653", 
-1:"base_frequency_g": "0.238808", 
-1:"base_frequency_t": "0.233665", 
\ No newline at end of file
+:base_frequency.base_frequency_a: 0.269874
+:base_frequency.base_frequency_c: 0.257653
+:base_frequency.base_frequency_g: 0.238808
+:base_frequency.base_frequency_t: 0.233665