Metavisitor: Trinity test in Use Case 2-2
Created: 2016-10-10 15:18:53
Last updated: 2016-10-10 16:01:19
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Inputs (14)
| Name |
Description |
| Input Dataset Collection |
|
| Protein Blast database |
|
| db_opts |
runtime parameter for tool NCBI BLAST+ blastx |
| query |
runtime parameter for tool NCBI BLAST+ blastx |
| blast |
runtime parameter for tool Parse blast output and compile hits |
| sequences |
runtime parameter for tool Parse blast output and compile hits |
| library |
runtime parameter for tool Bowtie2 |
| input |
runtime parameter for tool FASTQ to FASTA |
| input |
runtime parameter for tool Concatenate multiple datasets |
| switch |
runtime parameter for tool fasta - tabular |
| switch |
runtime parameter for tool fasta - tabular |
| inputs |
runtime parameter for tool Trinity |
| input |
runtime parameter for tool Regex Find And Replace |
| input |
runtime parameter for tool Filter sequences by length |
Steps (12)
| Name |
Tool |
Description |
| Input dataset collection |
None |
|
| Input dataset |
None |
|
| NCBI BLAST+ blastx |
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_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 |
|
| Bowtie2 |
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2 |
|
| FASTQ to FASTA |
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0 |
|
| 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 |
|
| Trinity |
toolshed.g2.bx.psu.edu/repos/anmoljh/trinityrnaseq/trinityrnaseq/r20140717 |
|
| Regex Find And Replace |
toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regex1/0.1.0 |
|
| Filter sequences by length |
toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1 |
|
Outputs (20)
| Name |
Type |
| output1 |
tabular |
| tabularOutput |
tabular |
| fastaOutput |
fasta |
| al_sequences |
fasta |
| un_sequences |
fasta |
| output_unaligned_reads_l |
fastqsanger |
| output_aligned_reads_l |
fastqsanger |
| output_aligned_reads_r |
fastqsanger |
| output_unaligned_reads_r |
fastqsanger |
| output |
bam |
| output_sam |
sam |
| mapping_stats |
txt |
| output |
fasta |
| out_file1 |
input |
| output |
fasta |
| output |
fasta |
| trinity_log |
txt |
| assembled_transcripts |
fasta |
| out_file1 |
input |
| output |
fasta |
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