Metavisitor: Workflow for Use Case 3-1
Created: 2016-05-13 08:36:21
Last updated: 2017-04-17 15:52:41
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Inputs (2)
| Name |
Description |
| Fever Patient Sequences collection |
|
| Nucleotide Viral Blast Database |
|
Steps (12)
| Name |
Tool |
Description |
| Input dataset collection |
None |
|
| Input dataset |
None |
|
| Parse blast output and compile hits |
toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3 |
|
| Concatenate multiple datasets |
toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2 |
|
| FASTQ to FASTA |
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0 |
|
| Trim sequences |
toolshed.g2.bx.psu.edu/repos/devteam/fastx_trimmer/cshl_fastx_trimmer/1.0.0 |
|
| 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/1.1.2.1 |
|
| sRbowtie |
toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2.1 |
|
| Oases_optimiser |
toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.2.1 |
|
| NCBI BLAST+ blastn |
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.08 |
|
Outputs (17)
| Name |
Type |
| tabularOutput |
tabular |
| fastaOutput |
fasta |
| al_sequences |
fasta |
| un_sequences |
fasta |
| out_file1 |
input |
| output |
fasta |
| output |
input |
| output |
fasta |
| output |
fasta |
| output |
tabular |
| aligned |
fasta |
| unaligned |
fasta |
| output |
tabular |
| aligned |
fasta |
| unaligned |
fasta |
| transcripts |
fasta |
| output1 |
tabular |
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Version 2 (latest)
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