| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/tximport/tximport/1.22.0 |
| toolshed.g2.bx.psu.edu/repos/iuc/tximport/tximport/1.20.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/tximport/tximport/0.1 |
| tximport |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bioconductor-tximport | 1.20.0 | package |
| bioconductor-genomicfeatures | 1.44.0 | package |
| r-getopt | 1.20.3 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
counts_file: ['salmon_sample2.tab', 'salmon_sample1.tab'] input_source_selector|input_source: salmon gene_id_source_selector|gff_source_selector|gff_tx2gene_selector|own_tx2gene: tx2gene.tab gene_id_source_selector|gff_source_selector|gff_tx2gene_selector|mapping_file_option: tx2gene gene_id_source_selector|gff_source_selector|gff_source: history gene_id_source_selector|gene_id_source: external_file counts_from_abundance: no |
name: value |
salmon_sample2.tab salmon_sample1.tab tx2gene.tab value |
| Test-2 |
counts_file: ['salmon_sample2.tab', 'salmon_sample1.tab'] input_source_selector|input_source: salmon gene_id_source_selector|gff_source_selector|gff_tx2gene_selector|own_gff: Araport11_subset.gff3 gene_id_source_selector|gff_source_selector|gff_tx2gene_selector|mapping_file_option: gff_gtf gene_id_source_selector|gff_source_selector|gff_source: history gene_id_source_selector|gene_id_source: external_file counts_from_abundance: no |
name: value |
salmon_sample2.tab salmon_sample1.tab Araport11_subset.gff3 value |
| Test-3 |
counts_file: ['salmon_sample2.tab', 'salmon_sample1.tab'] input_source_selector|input_source: salmon gene_id_source_selector|gff_source_selector|tx2gene: Ath_Araport11_subset gene_id_source_selector|gff_source_selector|gff_source: built-in gene_id_source_selector|gene_id_source: external_file counts_from_abundance: no |
name: value |
salmon_sample2.tab salmon_sample1.tab value |
| Test-4 |
counts_file: custom_sample.tab input_source_selector|tx_id_col: Transcript_id_here input_source_selector|abundance_col: Abundance_goes_here input_source_selector|counts_col: Here_goes_the_counts input_source_selector|length_col: Here_goes_the_length input_source_selector|input_source: none gene_id_source_selector|gff_source_selector|tx2gene: Ath_Araport11_subset gene_id_source_selector|gff_source_selector|gff_source: built-in counts_from_abundance: no |
name: value |
custom_sample.tab value |