Metavisitor: Workflow for Use Case 1-1
Created: 2016-05-13 07:49:17
Last updated: 2017-04-17 15:29:48
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Inputs (20)
| Name |
Description |
| Input Dataset Collection |
|
| viral nucleotide BLAST database (NCBI 19-10-2015) |
|
| db_opts |
runtime parameter for tool NCBI BLAST+ blastn |
| query |
runtime parameter for tool NCBI BLAST+ blastn |
| blast |
runtime parameter for tool Parse blast output and compile hits |
| sequences |
runtime parameter for tool Parse blast output and compile hits |
| inputSequences |
runtime parameter for tool cap3 |
| db_opts |
runtime parameter for tool NCBI BLAST+ blastn |
| query |
runtime parameter for tool NCBI BLAST+ blastn |
| guideSequence |
runtime parameter for tool blast_to_scaffold |
| blast_tab |
runtime parameter for tool blast_to_scaffold |
| sequences |
runtime parameter for tool blast_to_scaffold |
| input |
runtime parameter for tool Regex Find And Replace |
| input |
runtime parameter for tool Clip adapter |
| mask_data_file |
runtime parameter for tool NCBI BLAST+ makeblastdb |
| input_file |
runtime parameter for tool NCBI BLAST+ makeblastdb |
| input |
runtime parameter for tool Concatenate multiple datasets |
| switch |
runtime parameter for tool fasta - tabular |
| switch |
runtime parameter for tool fasta - tabular |
| input |
runtime parameter for tool sRbowtie |
Steps (16)
| Name |
Tool |
Description |
| Input dataset collection |
None |
|
| Input dataset |
None |
|
| NCBI BLAST+ blastn |
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06 |
|
| Parse blast output and compile hits |
toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3 |
|
| cap3 |
toolshed.g2.bx.psu.edu/repos/drosofff/msp_cap3/cap3/1.2.0 |
|
| NCBI BLAST+ blastn |
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06 |
|
| blast_to_scaffold |
toolshed.g2.bx.psu.edu/repos/drosofff/blast_to_scaffold/blast2scaffold/0.9.0 |
|
| Regex Find And Replace |
toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regex1/0.1.0 |
|
| Retrieve FASTA from NCBI |
toolshed.g2.bx.psu.edu/repos/drosofff/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/0.9.4 |
|
| Clip adapter |
toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6 |
|
| NCBI BLAST+ makeblastdb |
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.06 |
|
| Concatenate multiple datasets |
toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2 |
|
| fasta - tabular |
toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0 |
|
| fasta - tabular |
toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0 |
|
| sRbowtie |
toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2 |
|
| Oases_optimiser |
toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.5 |
|
Outputs (27)
| Name |
Type |
| output1 |
tabular |
| tabularOutput |
tabular |
| fastaOutput |
fasta |
| al_sequences |
fasta |
| un_sequences |
fasta |
| contigsandsinglets |
fasta |
| cap3stdout |
txt |
| contigs |
fasta |
| contigsqual |
txt |
| contigslink |
txt |
| ace |
txt |
| info |
txt |
| singlets |
txt |
| output1 |
tabular |
| output |
fasta |
| out_file1 |
input |
| outfilename |
fasta |
| logfile |
txt |
| output |
fasta |
| outfile |
data |
| out_file1 |
input |
| output |
fasta |
| output |
fasta |
| output |
tabular |
| aligned |
fasta |
| unaligned |
fasta |
| transcripts |
fasta |
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