fix(profiling): use yaml format aggreed on issue bioboxes#207

container/profiling/rfc.mkd

@@ -35,21 +35,22 @@ A biobox requires an input YAML with the following definition
 ~~~YAML
 version: 1.0.0
 arguments:
-  reads:
-    - format: bioboxes.org:/fastq
-      path: STRING
-  databases:
-    taxonomy:
-      path: STRING
-      format: bioboxes.org:/taxonomy_ncbi_dumps  
-  cache: STRING
+  - fastq:
+    - type: fastq
+      value: STRING
+  - databases:
+    - type: bioboxes.org:/taxonomy_ncbi_dumps 
+      value: STRING
+  - cache:
+    type: directory
+    value: STRING
 ~~~
 
 ##### Description:
 
 * **version**: The current version is specified directly under the heading.
 * **arguments**: The arguments field consists of the following fields 
-       * **reads**: An array of gzipped fastq sequence libraries.
+       * **fastq**: An array of gzipped fastq sequence libraries.
        * **databases**: The taxonomy database. A directory containing nodes.dmp and names.dmp. 
        * **cache**: Path to a cache directory.
 
@@ -62,11 +63,11 @@ arguments:
 
 ```YAML
   path: STRING
-  format: STRING
+  value: STRING
 ```
 
 * `path` means absolute path to file in container
-* `format` gives a machine-checkable type definition (will be transformed to YAML tag in future)
+* `value` gives a machine-checkable type definition
 
 ### Outputs
 
@@ -78,7 +79,7 @@ version: NUMBER.NUMBER.NUMBER
 arguments: 
     profiling:
        - path: STRING
-         format: bioboxes.org:/profling:0.9
+         value: bioboxes.org:/profling:0.9
 ~~~
 
 #### Description:
@@ -97,8 +98,7 @@ log.txt Logging information that is generated by the application inside the cont
 
 Any biobox based profiling tool accepts at least one of the following signatures:
 
-    fastq A -> profiling B
-    fastq A, database B -> profiling C
+    fastq A, database B, Maybe cache -> profiling C
 
 ### Example
 
@@ -107,12 +107,13 @@ This is an example biobox.yaml file:
 ~~~YAML
 version: 1.0.0
 arguments:
-  reads:
-    - format: bioboxes.org:/fastq
-      path: /path/to/fastq
-  databases:
-    taxonomy:
-      path: /path/to/ncbi_dump
-      format: bioboxes.org:/taxonomy_ncbi_dumps  
-  cache: /path/to/cache/directory
+  - fastq:
+    - type: fastq
+      value: /path/to/fastq
+  - database:
+    type: bioboxes.org:/taxonomy_ncbi_dumps
+    value: /path/to/ncbi_dump
+  - cache:
+    type: directory
+    value: /path/to/cache/directory
 ~~~