| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.14.1.2 |
| toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.11.2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.9.1 |
| toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.8.2 |
| toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.7.2 |
| salmon |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bzip2 | 1.0.6 | package |
| salmon | 0.11.2 | package |
| seqtk | 1.2 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
refTranscriptSource|ownFile: transcripts.fasta single_or_paired|single_or_paired_opts: paired single_or_paired|input_mate1: reads_1.fastq single_or_paired|input_mate2: reads_2.fastq refTranscriptSource|TranscriptSource: history |
attributes: name |
transcripts.fasta reads_1.fastq reads_2.fastq name |
| Test-2 |
refTranscriptSource|index: hg19_transcript_subset single_or_paired|single_or_paired_opts: paired single_or_paired|input_mate1: reads_1.fastq single_or_paired|input_mate2: reads_2.fastq refTranscriptSource|TranscriptSource: indexed |
attributes: name |
reads_1.fastq reads_2.fastq name |
| Test-3 |
refTranscriptSource|ownFile: transcripts.fasta single_or_paired|single_or_paired_opts: paired single_or_paired|input_mate1: reads_1.fastq.gz single_or_paired|input_mate2: reads_2.fastq.gz refTranscriptSource|TranscriptSource: history |
attributes: name |
transcripts.fasta reads_1.fastq.gz reads_2.fastq.gz name |
| Test-4 |
refTranscriptSource|ownFile: transcripts.fasta single_or_paired|single_or_paired_opts: paired single_or_paired|input_mate1: reads_1.fastq.bz2 single_or_paired|input_mate2: reads_2.fastq.bz2 refTranscriptSource|TranscriptSource: history |
attributes: name |
transcripts.fasta reads_1.fastq.bz2 reads_2.fastq.bz2 name |
| Test-5 |
single_or_paired|input_1: reads_both.fastq.bz2 single_or_paired|single_or_paired_opts: paired_interleaved refTranscriptSource|ownFile: transcripts.fasta refTranscriptSource|TranscriptSource: history |
attributes: name |
transcripts.fasta reads_both.fastq.bz2 name |
| Test-6 |
single_or_paired|input_1: reads_both.fastq.gz single_or_paired|single_or_paired_opts: paired_interleaved refTranscriptSource|ownFile: transcripts.fasta refTranscriptSource|TranscriptSource: history |
attributes: name |
transcripts.fasta reads_both.fastq.gz name |
| Test-7 |
single_or_paired|single_or_paired_opts: paired geneMap: gene_map.tab single_or_paired|input_mate1: reads_1.fastq single_or_paired|input_mate2: reads_2.fastq refTranscriptSource|TranscriptSource: history refTranscriptSource|ownFile: transcripts.fasta |
attributes: name attributes: name |
transcripts.fasta reads_1.fastq reads_2.fastq gene_map.tab name |
| Test-8 |
single_or_paired|input_1: paired collection single_or_paired|single_or_paired_opts: paired_collection geneMap: gene_map.tab refTranscriptSource|ownFile: transcripts.fasta refTranscriptSource|TranscriptSource: history |
attributes: name attributes: name |
transcripts.fasta reads_1.fastq reads_2.fastq gene_map.tab name |
| Test-9 |
single_or_paired|single_or_paired_opts: paired geneMap: gene_map.tab single_or_paired|input_mate1: reads_1.fastq single_or_paired|input_mate2: reads_2.fastq refTranscriptSource|TranscriptSource: history quasi_orphans|validateMappings: True refTranscriptSource|ownFile: transcripts.fasta |
attributes: name attributes: name |
transcripts.fasta reads_1.fastq reads_2.fastq gene_map.tab name |
| Test-10 |
single_or_paired|single_or_paired_opts: paired_collection geneMap: gene_map.tab single_or_paired|input_1: paired collection refTranscriptSource|TranscriptSource: history quasi_orphans|validateMappings: True refTranscriptSource|ownFile: transcripts.fasta |
attributes: name attributes: name |
transcripts.fasta reads_1.fastq reads_2.fastq gene_map.tab name |
| Test-11 |
single_or_paired|single_or_paired_opts: paired geneMap: gene_map.tab single_or_paired|input_mate1: reads_1.fastq single_or_paired|input_mate2: reads_2.fastq adv|useEM: True refTranscriptSource|TranscriptSource: history refTranscriptSource|ownFile: transcripts.fasta |
attributes: name attributes: name |
transcripts.fasta reads_1.fastq reads_2.fastq gene_map.tab name |
| Test-12 |
single_or_paired|single_or_paired_opts: paired_collection geneMap: gene_map.tab single_or_paired|input_1: paired collection adv|useEM: True refTranscriptSource|TranscriptSource: history refTranscriptSource|ownFile: transcripts.fasta |
attributes: name attributes: name |
transcripts.fasta reads_1.fastq reads_2.fastq gene_map.tab name |