validate.feature in scaffolder-tools-0.1.3

- old
+ new

@@ -1,76 +1,10 @@
 Feature: The scaffolder-validate binary
   In order to test inserts are being correctly added to a scaffold
   A user can use the scaffolder binary with the argument validate
   to test that inserts are correctly inserted
 
-  Scenario: The sequence file specified does not exist
-    Given a file named "scaffold.yml" with:
-      """
-      ---
-        -
-          sequence:
-            source: "seq"
-      """
-    When I call "scaffolder" with arguments "validate scaffold.yml missing_file"
-    Then the exit status should be 1
-    And the stderr should contain "Error. Sequence file not found:"
-
-  Scenario: The sequence file doesn't contain any thing
-    Given an empty file named "sequence.fna"
-    Given a file named "scaffold.yml" with:
-      """
-      ---
-        -
-          sequence:
-            source: "seq1"
-      """
-    When I call "scaffolder" with arguments "validate scaffold.yml sequence.fna"
-    Then the exit status should be 1
-    And the stderr should contain "Error. Sequence file is empty"
-
-  Scenario: The scaffold file specified does not exist
-    Given a file named "sequence.fna" with:
-      """
-      >seq
-      ATGGC
-      """
-    When I call "scaffolder" with arguments "validate missing_file sequence.fna"
-    Then the exit status should be 1
-    And the stderr should contain "Error. Scaffold file not found:"
-
-  Scenario: The scaffold file doesn't contain anything
-    Given an empty file named "scaffold.yml"
-    Given a file named "sequence.fna" with:
-      """
-      >seq
-      ATGGC
-      """
-    When I call "scaffolder" with arguments "validate scaffold.yml sequence.fna"
-    Then the exit status should be 1
-    And the stderr should contain "Error. Scaffold file is empty"
-
-  Scenario: One of the sequences specified in the scaffold is missing
-    Given a file named "sequence.fna" with:
-      """
-      >seq1
-      ATGGC
-      """
-    Given a file named "scaffold.yml" with:
-      """
-      ---
-        -
-          sequence:
-            source: "seq1"
-        -
-          sequence:
-            source: "seq2"
-      """
-    When I call "scaffolder" with arguments "validate scaffold.yml sequence.fna"
-    Then the exit status should be 1
-    And the stderr should contain "Error. Unknown sequence: seq2"
-
   Scenario: Validating a scaffold with no overlapping inserts
     Given a file named "sequence.fna" with:
       """
       >seq
       ATGGC
@@ -167,22 +101,22 @@
               source: ins2
 
       """
     When I call "scaffolder" with arguments "validate scaffold.yml sequence.fna"
     Then the exit status should be 0
-    And the stdout should contain exactly:
+    And the stdout yaml should contain exactly:
     """
-    --- 
-    - sequence-insert-overlap: 
-        inserts: 
+    ---
+    - sequence-insert-overlap:
+        source: seq
+        inserts:
         - open: 2
           close: 4
           source: ins1
         - open: 3
           close: 5
           source: ins2
-        source: seq
 
     """
 
   Scenario: Validating a scaffold with two sets of overlapping inserts
     Given a file named "sequence.fna" with:
@@ -218,28 +152,28 @@
               close: 9
               source: ins2
       """
     When I call "scaffolder" with arguments "validate scaffold.yml sequence.fna"
     Then the exit status should be 0
-    And the stdout should contain exactly:
+    And the stdout yaml should contain exactly:
     """
-    --- 
-    - sequence-insert-overlap: 
-        inserts: 
+    ---
+    - sequence-insert-overlap:
+        source: seq
+        inserts:
         - open: 2
           close: 4
           source: ins1
         - open: 3
           close: 5
           source: ins2
+    - sequence-insert-overlap:
         source: seq
-    - sequence-insert-overlap: 
-        inserts: 
+        inserts:
         - open: 6
           close: 8
           source: ins1
         - open: 7
           close: 9
           source: ins2
-        source: seq
 
     """