[med-svn] [fastaq] 01/01: Corrected EDAM annotation file
Steffen Möller
moeller at moszumanska.debian.org
Sun Jan 15 18:52:23 UTC 2017
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moeller pushed a commit to branch master
in repository fastaq.
commit fa06790a03733fc0fdc3759b3e9b4e8711fe1aa4
Author: Steffen Moeller <moeller at debian.org>
Date: Sun Jan 15 19:50:20 2017 +0100
Corrected EDAM annotation file
---
debian/upstream/edam | 505 ++++++++++++++++++++++-----------------------------
1 file changed, 218 insertions(+), 287 deletions(-)
diff --git a/debian/upstream/edam b/debian/upstream/edam
index 8867c27..b0c3b93 100644
--- a/debian/upstream/edam
+++ b/debian/upstream/edam
@@ -1,426 +1,357 @@
+---
ontology: EDAM (1.12)
topic:
- Bioinformatics
scopes:
- name: add_indels
function:
- - Sequence mutation and randomization
+ - Sequence mutation and randomization
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
outputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
- name: caf_to_fastq
function:
- - Formatting
+ - Formatting
inputs:
- - data: Sequence assembly report
- formats:
- - CAF
+ - data: Sequence assembly report
+ formats: [CAF]
outputs:
- - data: Sequence
- formats:
- - FASTQ
+ - data: Sequence
+ formats: [FASTQ]
- name: capillary_to_pairs
function:
- - Sequence file editing
+ - Sequence file editing
inputs:
- - data: Sequence
- formats:
- - FASTA
+ - data: Sequence
+ formats: [FASTA]
outputs:
- - data: Sequence
- formats:
- - FASTA
+ - data: Sequence
+ formats: [FASTA]
- name: chunker
function:
- - Splitting
+ - Splitting
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
outputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
- name: count_sequences
function:
- - File handling
+ - File handling
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
outputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
- name: deinterleave
function:
- - Splitting
+ - Splitting
inputs:
- - data: Sequence
- formats:
- - FASTA
+ - data: Sequence
+ formats: [FASTA]
outputs:
- - data: Sequence
- formats:
- - FASTA
+ - data: Sequence
+ formats: FASTA
- name: enumerate_names
function:
- - Sequence file editing
+ - Sequence file editing
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
outputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
- name: expand_nucleotides
function:
- - Sequence generation (nucleic acid)
+ - Sequence generation (nucleic acid)
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
outputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
- name: fasta_to_fastq
function:
- - Formatting
+ - Formatting
inputs:
- - data: Sequence
- formats:
- - FASTA
- - qual
+ - data: Sequence
+ formats:
+ - FASTA
+ - qual
outputs:
- - data: Sequence
- formats:
- - FASTQ
+ - data: Sequence
+ formats: [FASTQ]
- name: filter
function:
- - Sequence file editing
+ - Sequence file editing
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
outputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
- name: get_ids
function:
- - ID retrieval
+ - ID retrieval
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
outputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
- name: get_seq_flanking_gaps
function:
- - Sequence database search
+ - Sequence database search
inputs:
- - data: Sequence
- formats:
- - FASTA
+ - data: Sequence
+ formats: [FASTA]
outputs:
- - data: Sequence
- formats:
- - FASTA
+ - data: Sequence
+ formats: [FASTA]
- name: interleave
function:
- - Aggregation
+ - Aggregation
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
outputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
- name: make_random_contigs
function:
- - Random sequence generation
+ - Random sequence generation
outputs:
- - data: Sequence
- formats:
- - FASTQ
+ - data: Sequence
+ formats: FASTQ
- name: merge
function:
- - Aggregation
+ - Aggregation
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
outputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
- name: replace_bases
function:
- - Sequence mutation and randomization
+ - Sequence mutation and randomization
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
outputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
- name: reverse_complement
function:
- - Nucleic acid sequence reverse and complement
+ - Nucleic acid sequence reverse and complement
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
outputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
- name: scaffolds_to_contigs
function:
- - Sequence generation (nucleic acid)
+ - Sequence generation (nucleic acid)
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
outputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
- name: search_for_seq
function:
- - Sequence database search
+ - Sequence database search
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
outputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
- name: sequence_trim
function:
- - Sequence trimming
+ - Sequence trimming
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
outputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
- name: sort_by_size
function:
- - Sequence file editing
+ - Sequence file editing
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
outputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
- name: split_by_base_count
function:
- - Splitting
+ - Splitting
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
outputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
- name: strip_illumina_suffix
function:
- - Sequence file editing
+ - Sequence file editing
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
outputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
- name: to_fake_qual
function:
- - Generation
+ - Generation
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
outputs:
- - data: Sequence
- formats:
- - qual
+ - data: Sequence
+ formats:
+ - qual
- name: to_fasta
function:
- - Formatting
+ - Formatting
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
- - GFF3-seq
- - EMBL format
- - GenBank forat
- - PHYLIP format
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ - GFF3-seq
+ - EMBL format
+ - GenBank forat
+ - PHYLIP format
outputs:
- - data: Sequence
- formats:
- - FASTA
+ - data: Sequence
+ formats:
+ - FASTA
- name: to_mira_xml
function:
- - Generation
+ - Generation
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
outputs:
- - data: Sequence
- formats:
- - XML
+ - data: Sequence
+ formats:
+ - XML
- name: to_orfs_gff
function:
- - Coding region prediction
+ - Coding region prediction
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
outputs:
- - data: Sequence features
- formats:
- - GFF3
+ - data: Sequence features
+ formats:
+ - GFF3
- name: to_perfect_reads
function:
- - Generation
+ - Generation
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
outputs:
- - data: Sequence
- formats:
- - FASTQ
+ - data: Sequence
+ formats:
+ - FASTQ
- name: to_random_subset
function:
- - Random sequence generation
+ - Random sequence generation
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
outputs:
- - data: Sequence
- formats:
- - FASTQ
+ - data: Sequence
+ formats: FASTQ
- name: to_tiling_bam
function:
- - Generation
+ - Generation
inputs:
- - data: Sequence
- formats:
- - FASTA
+ - data: Sequence
+ formats: FASTA
outputs:
- - data: Alignment
- formats:
- - BAM
+ - data: Alignment
+ formats: [BAM]
- name: translate
function:
- - DNA translation
+ - DNA translation
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
outputs:
- - data: Sequence
- formats:
- - FASTA
+ - data: Sequence
+ formats: FASTA
- name: trim_Ns_at_end
function:
- - Sequence trimming
+ - Sequence trimming
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
outputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
- name: trim_contigs
function:
- - Sequence trimming
+ - Sequence trimming
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
outputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
- name: trim_ends
function:
- - Sequence trimming
+ - Sequence trimming
inputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
+ - data: Sequence
+ formats: [FASTA, FASTQ]
outputs:
- - data: Sequence
- formats:
- - FASTA
- - FASTQ
\ No newline at end of file
+ - data: Sequence
+ formats: [FASTA, FASTQ]
--
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