| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/tximport/tximport/1.20.0 |
| toolshed.g2.bx.psu.edu/repos/iuc/tximport/tximport/0.1 (this tool) |
| tximport |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bioconductor-tximport | not provided | package |
| bioconductor-genomicfeatures | 1.34.1 | package |
| r-getopt | 1.20.2 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
gene_id_source_selector|gff_source_selector|gff_tx2gene_selector|mapping_file_option: tx2gene counts_file: ['salmon_sample2.tab', 'salmon_sample1.tab'] gene_id_source_selector|gff_source_selector|gff_source: history input_source_selector|input_source: salmon counts_from_abundance: no gene_id_source_selector|gene_id_source: external_file gene_id_source_selector|gff_source_selector|gff_tx2gene_selector|own_tx2gene: tx2gene.tab |
attributes: name |
salmon_sample2.tab salmon_sample1.tab tx2gene.tab name |
| Test-2 |
counts_from_abundance: no counts_file: ['salmon_sample2.tab', 'salmon_sample1.tab'] gene_id_source_selector|gff_source_selector|gff_source: history gene_id_source_selector|gff_source_selector|gff_tx2gene_selector|own_gff: Araport11_subset.gff3 input_source_selector|input_source: salmon gene_id_source_selector|gff_source_selector|gff_tx2gene_selector|mapping_file_option: gff_gtf gene_id_source_selector|gene_id_source: external_file |
attributes: name |
salmon_sample2.tab salmon_sample1.tab Araport11_subset.gff3 name |
| Test-3 |
counts_file: ['salmon_sample2.tab', 'salmon_sample1.tab'] gene_id_source_selector|gff_source_selector|tx2gene: Ath_Araport11_subset gene_id_source_selector|gff_source_selector|gff_source: built-in input_source_selector|input_source: salmon counts_from_abundance: no gene_id_source_selector|gene_id_source: external_file |
attributes: name |
salmon_sample2.tab salmon_sample1.tab name |
| Test-4 |
input_source_selector|abundance_col: Abundance_goes_here counts_file: custom_sample.tab gene_id_source_selector|gff_source_selector|tx2gene: Ath_Araport11_subset gene_id_source_selector|gff_source_selector|gff_source: built-in input_source_selector|input_source: none input_source_selector|counts_col: Here_goes_the_counts input_source_selector|tx_id_col: Transcript_id_here counts_from_abundance: no input_source_selector|length_col: Here_goes_the_length |
attributes: name |
custom_sample.tab name |