Workflow: index sim seq
Fetched 2023-01-14 08:00:21 GMT
Verified with cwltool version 3.1.20221201130942
create sorted / filtered similarity file with feature sequences, and index by md5
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- 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/7b1df2ecce5a8727f2c546c5baa45c919edd8a76/CWL/Workflows/index_sim_seq.workflow.cwl
