| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.9.0+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.9.0+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.5.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.3.0+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.14.1.2+galaxy1 |
| 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 |
| toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.14.1 |
| 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 |
| salmon | 1.10.1 | package |
| seqtk | 1.3 | package |
| samtools | 1.16.1 | package |
| vpolo | 0.2.0 | package |
| pandas | 1.5.2 | package |
| graphviz | 3.0.0 | package |
| scipy | 1.9.3 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
quant_type|refTranscriptSource|s_index|fasta: transcripts.fasta quant_type|refTranscriptSource|TranscriptSource: history quant_type|input|single_or_paired|input_mate1: fastqs/reads_1.fastq quant_type|input|single_or_paired|input_mate2: fastqs/reads_2.fastq quant_type|input|single_or_paired|libtype|strandedness: U quant_type|input|single_or_paired|single_or_paired_opts: paired quant_type|bam_options|writeMappings: --writeMappings=./output/samout.sam quant_type|qtype: reads |
name: value |
transcripts.fasta fastqs/reads_1.fastq fastqs/reads_2.fastq value |
| Test-2 |
quant_type|refTranscriptSource|s_index|fasta: transcripts.fasta quant_type|refTranscriptSource|TranscriptSource: history quant_type|bam_options|writeMappings: --writeMappings=./output/samout.sam quant_type|qtype: reads |
name: value |
transcripts.fasta value |
| Test-3 |
quant_type|refTranscriptSource|s_index|fasta: transcripts.fasta quant_type|refTranscriptSource|TranscriptSource: history quant_type|qtype: reads |
name: value |
transcripts.fasta value |
| Test-4 |
quant_type|refTranscriptSource|s_index|fasta: transcripts.fasta quant_type|refTranscriptSource|TranscriptSource: history quant_type|qtype: reads |
name: value |
transcripts.fasta value |
| Test-5 |
quant_type|afile: salmonbam.bam quant_type|transcript: transcripts.fasta quant_type|noErrorModel: True quant_type|numErrorBins: 5 quant_type|sampleOut: True quant_type|sampleUnaligned: True quant_type|qtype: alignment |
name: value |
salmonbam.bam transcripts.fasta value |
| Test-6 |
quant_type|afile: salmonbam.bam quant_type|ont: True quant_type|transcript: transcripts.fasta quant_type|noErrorModel: True quant_type|numErrorBins: 5 quant_type|sampleOut: True quant_type|sampleUnaligned: True quant_type|qtype: alignment |
salmonbam.bam transcripts.fasta |
|
| Test-7 |
quant_type|refTranscriptSource|s_index|fasta: transcripts.fasta quant_type|refTranscriptSource|TranscriptSource: history quant_type|discardOrphansQuasi: False quant_type|validmap|validateMappings: --validateMappings quant_type|dovetail: True quant_type|recoverOrphans: True quant_type|qtype: reads |
name: value |
transcripts.fasta value |
| Test-8 |
quant_type|refTranscriptSource|s_index|fasta: transcripts.fasta quant_type|refTranscriptSource|TranscriptSource: history quant_type|qtype: reads seqBias: True gcBias: True adv|dumpEq: True adv|minAssignedFrags: 10 adv|initUniform: True adv|noLengthCorrection: False adv|useEM: True adv|noGammaDraw: True |
name: value |
transcripts.fasta value |
| Test-9 |
quant_type|refTranscriptSource|index: hg19_transcript_subset quant_type|refTranscriptSource|TranscriptSource: indexed quant_type|input|single_or_paired|input_mate1: fastqs/reads_1.fastq quant_type|input|single_or_paired|input_mate2: fastqs/reads_2.fastq quant_type|input|single_or_paired|single_or_paired_opts: paired quant_type|qtype: reads |
name: value |
fastqs/reads_1.fastq fastqs/reads_2.fastq value |
| Test-10 |
quant_type|refTranscriptSource|s_index|fasta: transcripts.fasta quant_type|refTranscriptSource|TranscriptSource: history quant_type|bam_options|writeQualities: True quant_type|bam_options|writeMappings: --writeMappings=./output/samout.sam quant_type|qtype: reads |
name: value |
transcripts.fasta value |
| Test-11 |
quant_type|refTranscriptSource|s_index|fasta: transcripts.fasta quant_type|refTranscriptSource|s_index|genome: genome.fasta quant_type|refTranscriptSource|TranscriptSource: history quant_type|input|single_or_paired|input_mate1: fastqs/reads_1.fastq quant_type|input|single_or_paired|input_mate2: fastqs/reads_2.fastq quant_type|input|single_or_paired|libtype|strandedness: U quant_type|input|single_or_paired|single_or_paired_opts: paired quant_type|bam_options|writeMappings: --writeMappings=./output/samout.sam quant_type|qtype: reads |
name: value |
transcripts.fasta genome.fasta fastqs/reads_1.fastq fastqs/reads_2.fastq value |
| Test-12 |
quant_type|refTranscriptSource|s_index|fasta: transcripts.fasta quant_type|refTranscriptSource|TranscriptSource: history quant_type|input|single_or_paired|input_1: fastqs/reads_both.fastq.bz2 quant_type|input|single_or_paired|libtype|strandedness: U quant_type|input|single_or_paired|single_or_paired_opts: paired_interleaved quant_type|bam_options|writeMappings: --writeMappings=./output/samout.sam quant_type|qtype: reads |
name: value |
transcripts.fasta fastqs/reads_both.fastq.bz2 value |