switch from TOML to YAML

Author: a-frantz

data_structures/flag_filter.toml

@@ -0,0 +1,43 @@
+validate_string_is_12bit_int:
+  - name: decimal_passes
+    inputs:
+      - number: "5"
+  - name: hexadecimal_passes
+    inputs:
+      - number: "0x900"
+    tests:
+      stdout:
+        contains: Input number (0x900) is valid
+  - name: too_big_hexadecimal_fails
+    inputs:
+      - number: "0x1000"
+    tests:
+      exit_code: 42
+      stderr:
+        contains: Input number (0x1000) is invalid
+  - name: too_big_decimal_fails
+    inputs:
+      - number: "4096"
+    tests:
+      exit_code: 42
+      stderr:
+        contains:
+          - Input number (4096) interpreted as decimal
+          - But number must be less than 4096!
+validate_flag_filter:
+  - name: valid_FlagFilter_passes
+    inputs:
+      - flags:
+          include_if_all: "3"
+          exclude_if_any: "0xF04"
+          include_if_any: "03"
+          exclude_if_all: "4095"
+  - name: invalid_FlagFilter_fails
+    inputs:
+      - flags:
+          include_if_all: ""
+          exclude_if_any: this is not a number
+          include_if_any: "000000000011"
+          exclude_if_all: "4095"
+    tests:
+      should_fail: true

data_structures/flag_filter.yaml

@@ -0,0 +1,9 @@
+merge_sam_files:
+  - name: Merge works
+    inputs:
+      - bams:
+          - $FIXTURES/test1.bam
+          - $FIXTURES/test2.bam
+      - prefix: test.merged
+    tests:
+      custom: quickcheck.sh

tools/picard.toml

@@ -0,0 +1,34 @@
+bam_to_fastq:
+  - name: kitchen_sink
+    inputs:
+      - bam:
+          - $FIXTURES/test1.bam
+          - $FIXTURES/test2.bam
+          - $FIXTURES/test3.bam
+        bam_index:
+          - $FIXTURES/test1.bam.bai
+          - $FIXTURES/test2.bam.bai
+          - $FIXTURES/test3.bam.bai
+      - bitwise_filter:
+          - include_if_all: "0x0"
+            exclude_if_any: "0x900"
+            include_if_any: "0x0"
+            exclude_if_all: "0x0"
+          - include_if_all: "00"
+            exclude_if_any: "0x904"
+            include_if_any: "3"
+            exclude_if_all: "0"
+      - paired_end:
+          - true
+          - false
+      - retain_collated_bam:
+          - true
+          - false
+      - append_read_number:
+          - true
+          - false
+      - output_singletons:
+          - true
+          - false
+      - prefix:
+          - kitchen_sink_test