[med-svn] r23974 - trunk/packages/bowtie/trunk/debian/upstream

[Steffen Möller]

Author: moeller
Date: 2017-08-29 19:08:55 +0000 (Tue, 29 Aug 2017)
New Revision: 23974

Modified:
   trunk/packages/bowtie/trunk/debian/upstream/edam
Log:
Correcting semantics, syntax is yamllint clean.


Modified: trunk/packages/bowtie/trunk/debian/upstream/edam
===================================================================
--- trunk/packages/bowtie/trunk/debian/upstream/edam	2017-08-28 18:46:21 UTC (rev 23973)
+++ trunk/packages/bowtie/trunk/debian/upstream/edam	2017-08-29 19:08:55 UTC (rev 23974)
@@ -1,64 +1,57 @@
 ---
 ontology: EDAM (1.13)
 topic:
- - Genomics
+  - Genomics
 scopes:
- - name: summary
-   function:
-    - operation_3211 Genome indexing
-    - operation_0292 Sequence alignment generation
-   inputs:
-    - data_2975 Nucleic acid sequence (raw)
-    - format_1929 FASTA
-    - format_1930 FASTQ
-   outputs:
-    - data_1383 Sequence alignment (nucleic acid)
-    - format_2573 SAM
- - name: bowtie-build
-   function: operation_3212 Genome indexing (Burrows-Wheeler)
-   inputs:
-    - data_2975 Nucleic acid sequence (raw)
-    - format_1929 FASTA
-   outputs:
-    - data_3210 Genome index
-    - ??? Bowtie index format EBWT
-    - ??? Bowtie long index format EBTWL
- - name: bowtie-inspect
-   function:
-    - operation_1813 Sequence retrieval
-    - operation_0304 Metadata retrieval
-    - operation_0228 Data index analysis
-   inputs:
-    - data_3210 Genome index
-    - ??? Bowtie index format EBWT
-    - ??? Bowtie long index format EBTWL
-   outputs:
-    - data_2975 Nucleic acid sequence (raw)
-    - format_1929 FASTA
-    - format_1964 plain text format (unformatted)
- - name: bowtie
-   function:
-    - operation_0350 Sequence database search (by sequence using word-based methods)
-    - operation_0292 Sequence alignment generation
-   inputs:
-    - data_3210 Genome index
-    - data_2975 Nucleic acid sequence (raw)
-    - format_1964 plain text format (unformatted)
-    - format_1929 FASTA
-    - format_1930 FASTQ
-   outputs:
-    - data_1383 Sequence alignment (nucleic acid)
-    - data_0867 Sequence alignment report
-    - format_2573 SAM
-    - ??? Bowtie alignment report format
- - name: FIXME remainings of blody syntax errors
-   function:
-    - operation_3212 Genome indexing (Burrows-Wheeler)
-    - operation_0292 Sequence alignment generation
-   inputs:
-    - data_2975 Nucleic acid sequence (raw)
-    - format_1929 FASTA
-    - format_1930 FASTQ
-   outputs:
-    - data_1383 Sequence alignment (nucleic acid)
-    - format_2573 SAM
+  - name: summary
+    function:
+      - Genome indexing
+      - Sequence alignment generation
+    input:
+      - data: Nucleic acid sequence (raw)
+        format: [FASTA, FASTQ]
+    output:
+      - data: Sequence alignment (nucleic acid)
+        format: [SAM]
+  - name: bowtie-build
+    function: Genome indexing (Burrows-Wheeler)
+    input:
+      - data: Nucleic acid sequence (raw)
+        format: [FASTA]
+    outputs:
+      - data: Genome index
+        format:
+          - Bowtie index format EBWT
+          - Bowtie long index format EBTWL
+  - name: bowtie-inspect
+    function:
+      - Sequence retrieval
+      - Metadata retrieval
+      - Data index analysis
+    inputs:
+      - data: Genome index
+        format:
+          - Bowtie index format EBWT
+          - Bowtie long index format EBTWL
+    outputs:
+      - data: Nucleic acid sequence (raw)
+        format:
+          - FASTA
+          - plain text format (unformatted)
+  - name: bowtie
+    function:
+      - Sequence database search (by sequence using word-based methods)
+      - Sequence alignment generation
+    inputs:
+      - data: Genome index
+      - data: Nucleic acid sequence (raw)
+        format:
+          - plain text format (unformatted)
+          - FASTA
+          - FASTQ
+    outputs:
+      - data: Sequence alignment (nucleic acid)
+      - data: Sequence alignment report
+        format:
+          - SAM
+          - Bowtie alignment report format