| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/trinity/abundance_estimates_to_matrix/2.1.1.1 |
| toolshed.g2.bx.psu.edu/repos/iuc/trinity/abundance_estimates_to_matrix/2.1.1 (this tool) |
| abundance_estimates_to_matrix |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| trinity | 2.1.1 | package |
| bowtie | 1.1.2 | package |
| samtools | 1.2 | package |
| edger | 3.12.0 | package |
| bioconductor-edger | 3.12.0 | package |
| rsem | 1.2.28 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
samples_1|sample_name: sample_B additional_params|cross_sample_norm: TMM est_method: RSEM samples_0|sample_name: sample_A samples_1|file: count/rsem_bowtie/RSEM.genes_B.results samples_0|file: count/rsem_bowtie/RSEM.genes.results |
trans_counts: None TPM_no_norm: None norm: None |
count/rsem_bowtie/RSEM.genes.results count/rsem_bowtie/RSEM.genes_B.results |
| Test-2 |
samples_1|sample_name: sample_B additional_params|cross_sample_norm: TMM est_method: RSEM samples_0|sample_name: sample_A samples_1|file: count/rsem_bowtie2/RSEM.genes_B.results samples_0|file: count/rsem_bowtie2/RSEM.genes.results |
trans_counts: None TPM_no_norm: None norm: None |
count/rsem_bowtie2/RSEM.genes.results count/rsem_bowtie2/RSEM.genes_B.results |
| Test-3 |
samples_1|sample_name: sample_B additional_params|cross_sample_norm: TMM est_method: eXpress samples_0|sample_name: sample_A samples_1|file: count/express_bowtie/results_B.xprs.genes samples_0|file: count/express_bowtie/results.xprs.genes |
trans_counts: None TPM_no_norm: None norm: None |
count/express_bowtie/results.xprs.genes count/express_bowtie/results_B.xprs.genes |
| Test-4 |
samples_1|sample_name: sample_B additional_params|cross_sample_norm: UpperQuartile est_method: RSEM samples_0|sample_name: sample_A samples_1|file: count/rsem_bowtie/RSEM.genes_B.results samples_0|file: count/rsem_bowtie/RSEM.genes.results |
trans_counts: None TPM_no_norm: None norm: matrix.UpperQuartile.EXPR.matrix |
count/rsem_bowtie/RSEM.genes.results count/rsem_bowtie/RSEM.genes_B.results count/matrix_rsem_bowtie_UpperQuartile/matrix.UpperQuartile.EXPR.matrix |
| Test-5 |
samples_1|sample_name: sample_B additional_params|cross_sample_norm: none est_method: RSEM samples_0|sample_name: sample_A samples_1|file: count/rsem_bowtie/RSEM.genes_B.results samples_0|file: count/rsem_bowtie/RSEM.genes.results |
trans_counts: None TPM_no_norm: None |
count/rsem_bowtie/RSEM.genes.results count/rsem_bowtie/RSEM.genes_B.results |