[med-svn] [fastaq] 01/01: add EDAM annotation
Sascha Steinbiss
sascha at steinbiss.name
Fri Feb 5 16:23:34 UTC 2016
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sascha-guest pushed a commit to branch master
in repository fastaq.
commit e9db6dc9e80c7c10cd63c6bfc27918fcc13a22bb
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Fri Feb 5 16:23:22 2016 +0000
add EDAM annotation
---
debian/upstream/edam | 426 +++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 426 insertions(+)
diff --git a/debian/upstream/edam b/debian/upstream/edam
new file mode 100644
index 0000000..8867c27
--- /dev/null
+++ b/debian/upstream/edam
@@ -0,0 +1,426 @@
+ontology: EDAM (1.12)
+topic:
+ - Bioinformatics
+scopes:
+ - name: add_indels
+ function:
+ - Sequence mutation and randomization
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ - name: caf_to_fastq
+ function:
+ - Formatting
+ inputs:
+ - data: Sequence assembly report
+ formats:
+ - CAF
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTQ
+ - name: capillary_to_pairs
+ function:
+ - Sequence file editing
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - name: chunker
+ function:
+ - Splitting
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ - name: count_sequences
+ function:
+ - File handling
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ - name: deinterleave
+ function:
+ - Splitting
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - name: enumerate_names
+ function:
+ - Sequence file editing
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ - name: expand_nucleotides
+ function:
+ - Sequence generation (nucleic acid)
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ - name: fasta_to_fastq
+ function:
+ - Formatting
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - qual
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTQ
+ - name: filter
+ function:
+ - Sequence file editing
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ - name: get_ids
+ function:
+ - ID retrieval
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ - name: get_seq_flanking_gaps
+ function:
+ - Sequence database search
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - name: interleave
+ function:
+ - Aggregation
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ - name: make_random_contigs
+ function:
+ - Random sequence generation
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTQ
+ - name: merge
+ function:
+ - Aggregation
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ - name: replace_bases
+ function:
+ - Sequence mutation and randomization
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ - name: reverse_complement
+ function:
+ - Nucleic acid sequence reverse and complement
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ - name: scaffolds_to_contigs
+ function:
+ - Sequence generation (nucleic acid)
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ - name: search_for_seq
+ function:
+ - Sequence database search
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ - name: sequence_trim
+ function:
+ - Sequence trimming
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ - name: sort_by_size
+ function:
+ - Sequence file editing
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ - name: split_by_base_count
+ function:
+ - Splitting
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ - name: strip_illumina_suffix
+ function:
+ - Sequence file editing
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ - name: to_fake_qual
+ function:
+ - Generation
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - qual
+ - name: to_fasta
+ function:
+ - Formatting
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ - GFF3-seq
+ - EMBL format
+ - GenBank forat
+ - PHYLIP format
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - name: to_mira_xml
+ function:
+ - Generation
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - XML
+ - name: to_orfs_gff
+ function:
+ - Coding region prediction
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence features
+ formats:
+ - GFF3
+ - name: to_perfect_reads
+ function:
+ - Generation
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTQ
+ - name: to_random_subset
+ function:
+ - Random sequence generation
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTQ
+ - name: to_tiling_bam
+ function:
+ - Generation
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ outputs:
+ - data: Alignment
+ formats:
+ - BAM
+ - name: translate
+ function:
+ - DNA translation
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - name: trim_Ns_at_end
+ function:
+ - Sequence trimming
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ - name: trim_contigs
+ function:
+ - Sequence trimming
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ - name: trim_ends
+ function:
+ - Sequence trimming
+ inputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
+ outputs:
+ - data: Sequence
+ formats:
+ - FASTA
+ - FASTQ
\ No newline at end of file
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