[med-svn] r18504 - trunk/packages/bowtie/trunk/debian/upstream

[Timothy Booth]

Author: tbooth-guest
Date: 2014-11-21 08:38:57 +0000 (Fri, 21 Nov 2014)
New Revision: 18504

Added:
   trunk/packages/bowtie/trunk/debian/upstream/edam
Modified:
   trunk/packages/bowtie/trunk/debian/upstream/metadata
Log:
Experimenting with adding EDAM tags (http://bioportal.bioontology.org/ontologies/EDAM)
to this package.


Added: trunk/packages/bowtie/trunk/debian/upstream/edam
===================================================================
--- trunk/packages/bowtie/trunk/debian/upstream/edam	                        (rev 0)
+++ trunk/packages/bowtie/trunk/debian/upstream/edam	2014-11-21 08:38:57 UTC (rev 18504)
@@ -0,0 +1,47 @@
+topic: topic_0622 Genomics
+scope: summary
+ function: operation_3212 Genome indexing (Burrows-Wheeler)
+ 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_3212 Genome indexing (Burrows-Wheeler)
+ 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_3212 Genome indexing (Burrows-Wheeler)
+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

Modified: trunk/packages/bowtie/trunk/debian/upstream/metadata
===================================================================
--- trunk/packages/bowtie/trunk/debian/upstream/metadata	2014-11-21 07:10:14 UTC (rev 18503)
+++ trunk/packages/bowtie/trunk/debian/upstream/metadata	2014-11-21 08:38:57 UTC (rev 18504)
@@ -1,5 +1,5 @@
 Reference:
- author: Ben Langmead and Cole Trapnell and Mihai Pop and Steven L Salzberg 
+ author: Ben Langmead and Cole Trapnell and Mihai Pop and Steven L Salzberg
  title: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
  journal: Genome Biology
  volume: 10