Workflow: index sim seq
create sorted / filtered similarity file with feature sequences, and index by md5
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
BSD 2-clause "Simplified" License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
jobid | String | ||
clustMaps | File[] | ||
filterSims | File[] | ||
featureSeqs | File[] |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
catSeqs |
../Tools/cat.tool.cwl
(CommandLineTool)
|
GNU cat |
Concatenate FILE(s) to standard output |
sortSeqs |
../Tools/seqUtil.tool.cwl
(CommandLineTool)
|
seqUtil |
Utility tool for various sequence file transformations. |
sortSims |
../Tools/sort.tool.cwl
(CommandLineTool)
|
GNU sort |
sort text file base on given field(s) |
addSeq2Sim |
../Tools/add_seq2sims.tool.cwl
(CommandLineTool)
|
uncluster sims |
append feature sequence to each hit line of similarity file >add_seq2sims --seq_file --in_sim |
sortSimSeq |
../Tools/sort.tool.cwl
(CommandLineTool)
|
GNU sort |
sort text file base on given field(s) |
indexSimSeq |
../Tools/index_sims_file_md5.tool.cwl
(CommandLineTool)
|
index sims by md5 |
index m8 format blast file by 2nd column (sorted required) return: value, seek, length for each record >index_sims_file_md5 --in_file <input> --out_file <outName> --md5_num <number> |
unclusterSims |
../Tools/uncluster_sims.tool.cwl
(CommandLineTool)
|
uncluster sims |
expand out similarity file (blast m8) by turning each cluster seed hit into a hit per cluster member >uncluster_sims.py <input> <outName> --cfile <cluster> --position <position> |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
indexOut | File | ||
simSeqOut | File |
Permalink:
https://w3id.org/cwl/view/git/6c5d0068bdb4f19a36a653c39964aefb9e5a7b1b/CWL/Workflows/index_sim_seq.workflow.cwl