| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.11.2 |
| toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.14.1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.11.2 |
| 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 |
| seqtk | 1.2 | package |
| salmon | 0.14.1 | package |
| samtools | 1.9 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
quant_type|writeMappings: True quant_type|qtype: reads quant_type|refTranscriptSource|s_index|fasta: transcripts.fasta quant_type|refTranscriptSource|TranscriptSource: history |
attributes: name |
transcripts.fasta name |
| Test-2 |
quant_type|qtype: reads quant_type|refTranscriptSource|s_index|fasta: transcripts.fasta quant_type|refTranscriptSource|TranscriptSource: history |
attributes: name |
transcripts.fasta name |
| Test-3 |
quant_type|qtype: reads quant_type|refTranscriptSource|s_index|fasta: transcripts.fasta quant_type|refTranscriptSource|TranscriptSource: history |
attributes: name |
transcripts.fasta name |
| Test-4 |
quant_type|sampleUnaligned: True quant_type|sampleOut: True quant_type|transcript: transcripts.fasta quant_type|noErrorModel: True quant_type|numErrorBins: 5 quant_type|qtype: alignment quant_type|afile: salmonbam.bam |
attributes: name |
salmonbam.bam transcripts.fasta name |
| Test-5 |
quant_type|discardOrphansQuasi: False quant_type|refTranscriptSource|s_index|fasta: transcripts.fasta quant_type|dovetail: True quant_type|refTranscriptSource|TranscriptSource: history quant_type|recoverOrphans: True quant_type|qtype: reads quant_type|validmap|validateMappings: True |
attributes: name |
transcripts.fasta name |
| Test-6 |
adv|initUniform: True adv|minAssignedFrags: 10 quant_type|refTranscriptSource|s_index|fasta: transcripts.fasta adv|useEM: True adv|dumpEq: True quant_type|refTranscriptSource|TranscriptSource: history seqBias: True quant_type|qtype: reads gcBias: True adv|noLengthCorrection: False adv|noGammaDraw: True |
attributes: name |
transcripts.fasta name |
| Test-7 |
quant_type|input|single_or_paired|strandedness: U quant_type|refTranscriptSource|index: hg19_transcript_subset quant_type|refTranscriptSource|TranscriptSource: indexed quant_type|qtype: reads quant_type|input|single_or_paired|single_or_paired_opts: paired quant_type|input|single_or_paired|input_mate1: fastqs/reads_1.fastq quant_type|input|single_or_paired|input_mate2: fastqs/reads_2.fastq |
attributes: name |
fastqs/reads_1.fastq fastqs/reads_2.fastq name |