[med-svn] [bowtie2] 01/01: Corrected EDAM annotation file

[Steffen Möller]

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moeller pushed a commit to branch master
in repository bowtie2.

commit 71862e37a5a83219d0c23639794d446081adf44a
Author: Steffen Moeller <moeller at debian.org>
Date:   Sun Jan 15 19:16:18 2017 +0100

    Corrected EDAM annotation file
---
 debian/upstream/edam | 100 +++++++++++++++++++++++++++------------------------
 1 file changed, 53 insertions(+), 47 deletions(-)

diff --git a/debian/upstream/edam b/debian/upstream/edam
index e55d751..ee98e00 100644
--- a/debian/upstream/edam
+++ b/debian/upstream/edam
@@ -1,48 +1,54 @@
+---
 ontology: EDAM (1.13)
-topic: topic_0622 Genomics
-scope: summary
- function: operation_3211 Genome indexing
- function: operation_0292 Sequence alignment generation
- input: data_2975 Nucleic acid sequence (raw)
- input: format_1929 FASTA
- input: format_1930 FASTQ
- output: data_1383 Sequence alignment (nucleic acid)
- output: format_2573 SAM
-scope: bowtie-build
- function: operation_3211 Genome indexing
- input: data_2975 Nucleic acid sequence (raw)
- input: format_1929 FASTA
- output: data_3210 Genome index
- output: ??? Bowtie index format EBWT
- output: ??? Bowtie long index format EBTWL
-scope: bowtie-inspect
- function: operation_1813 Sequence retrieval
- function: operation_0304 Metadata retrieval
- function: operation_0228 Data index analysis
- input: data_3210 Genome index
- input: ??? Bowtie index format EBWT
- input: ??? Bowtie long index format EBTWL
- output: data_2975 Nucleic acid sequence (raw)
- output: format_1929 FASTA
- output: format_1964 plain text format (unformatted)
-scope: bowtie
- function: operation_0350 Sequence database search (by sequence using word-based methods)
- function: operation_0292 Sequence alignment generation
- input: data_3210 Genome index
- input: data_2975 Nucleic acid sequence (raw)
- input: format_1964 plain text format (unformatted)
- input: format_1929 FASTA
- input: format_1930 FASTQ
- output: data_1383 Sequence alignment (nucleic acid)
- output: data_0867 Sequence alignment report
- output: format_2573 SAM
- output: ??? Bowtie alignment report format
-
-topic: topic_0622 Genomics
-function: operation_3211 Genome indexing
-function: operation_0292 Sequence alignment generation
-input: data_2975 Nucleic acid sequence (raw)
-input: format_1929 FASTA
-input: format_1930 FASTQ
-output: data_1383 Sequence alignment (nucleic acid)
-output: format_2573 SAM
+topic: Genomics
+scopes:
+  - 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
+    input:
+      - data: Nucleic acid sequence (raw)
+        format: [FASTA]
+    output:
+      - data: Genome index
+        format:
+          - ebwt
+          - ebwtl
+  - name: bowtie-inspect
+    function:
+      - Sequence retrieval
+      - Metadata retrieval
+      - Data index analysis
+    input:
+      - data: Genome index
+        format: [ebtw, ebtwl]
+    output:
+      - data: Nucleic acid sequence (raw)
+        output: [FASTA, plain text format (unformatted)]
+  - name: bowtie
+    function:
+      - Sequence database search (by sequence using word-based methods)
+      - Sequence alignment generation
+    input:
+      - data: Genome index
+        format: [ebtw, ebtwl]
+      - data: Nucleic acid sequence (raw)
+        format:
+          - plain text format (unformatted)
+          - FASTA
+          - FASTQ
+    output:
+      - data: Sequence alignment (nucleic acid)
+        format: SAM
+      - data: Sequence alignment report
+        format:
+          - plain text format (unformatted)
+          - Bowtie alignment report format

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