Workflow: tRNA_selection.cwl

Fetched 2019-12-07 04:20:28 GMT
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Inputs

ID Type Title Doc
indexed_sequences File [FASTA]
model File [HMMER format] tRNA model to search with

Steps

ID Runs Label Doc
extract_coord_lines
extract_coord_lines.cwl (CommandLineTool)
extract_coordinates
tRNA_selection.cwl#extract_coordinates/extract_coordinates (CommandLineTool)
nhmmer
nhmmer.cwl (CommandLineTool)
search profile(s) against a sequence database
sort_matches
RevReadSort.cwl (CommandLineTool)
fetch_aligned_sequences
esl-sfetch-manyseqs.cwl (CommandLineTool)
extract by names from an indexed sequence file

https://github.com/EddyRivasLab/easel

reformat_matches
oneLineFasta.cwl (CommandLineTool)

reformats FASTA. single line sequence, adds 'length=' to header drops seqs with identical IDs (up until the first `/`)

Outputs

ID Type Label Doc
matching_sequences File [FASTA]
hmmer_search_results File
Permalink: https://w3id.org/cwl/view/git/f6b5196bd493b0872ee6e63aa3499738bb7d53d6/tools/tRNA_selection.cwl