| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/cummerbund_to_tabular/cummerbund_to_cuffdiff/1.0.1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/cummerbund_to_tabular/cummerbund_to_cuffdiff/1.0.0 |
| cummerbund_to_cuffdiff |
| Requirements (dependencies defined in the <requirements> tag set) |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
tables: ['--tables cds_count', '--tables cds_diff', '--tables cds_exp_diff', '--tables cds_fpkm', '--tables cds_rg', '--tables gene_exp_diff', '--tables genes_count', '--tables genes_fpkm', '--tables gene_rg', '--tables isoform_exp_diff', '--tables isoform_count', '--tables isoform_fpkm', '--tables isoform_rg', '--tables promoters_diff', '--tables read_groups', '--tables run_info', '--tables splicing_diff', '--tables tss_group_exp', '--tables tss_count_tracking', '--tables tss_fpkm', '--tables tss_rg', '--tables var_model'] input_database: cuffdiff_out.sqlite |
cds_count_output: cds_count.tabular cds_diff_output: cds_diff.tabular cds_exp_diff_output: cds_exp_diff.tabular cds_fpkm_output: cds_fpkm.tabular cds_rg_output: cds_rg.tabular gene_exp_diff_output: gene_exp_diff.tabular genes_count_output: genes_count.tabular genes_fpkm_output: genes_fpkm.tabular gene_rg_output: gene_rg.tabular isoform_exp_diff_output: isoform_exp_diff.tabular isoform_count_output: isoform_count.tabular isoform_fpkm_output: isoform_fpkm.tabular isoform_rg_output: isoform_rg.tabular promoters_diff_output: promoters_diff.tabular read_groups_output: read_groups.tabular run_info_output: run_info.tabular splicing_diff_output: splicing_diff.tabular tss_group_exp_output: tss_group_exp.tabular tss_count_tracking_output: tss_count_tracking.tabular tss_fpkm_output: tss_fpkm.tabular tss_rg_output: tss_rg.tabular var_model_output: var_model.tabular |
cuffdiff_out.sqlite cds_count.tabular cds_diff.tabular cds_exp_diff.tabular cds_fpkm.tabular cds_rg.tabular gene_exp_diff.tabular genes_count.tabular genes_fpkm.tabular gene_rg.tabular isoform_exp_diff.tabular isoform_count.tabular isoform_fpkm.tabular isoform_rg.tabular promoters_diff.tabular read_groups.tabular run_info.tabular splicing_diff.tabular tss_group_exp.tabular tss_count_tracking.tabular tss_fpkm.tabular tss_rg.tabular var_model.tabular |
| Test-2 |
tables: --tables cds_count input_database: cuffdiff_out.sqlite |
cds_count_output: cds_count.tabular |
cuffdiff_out.sqlite cds_count.tabular |
| Test-3 |
tables: --tables cds_diff input_database: cuffdiff_out.sqlite |
cds_diff_output: cds_diff.tabular |
cuffdiff_out.sqlite cds_diff.tabular |
| Test-4 |
tables: --tables cds_exp_diff input_database: cuffdiff_out.sqlite |
cds_exp_diff_output: cds_exp_diff.tabular |
cuffdiff_out.sqlite cds_exp_diff.tabular |
| Test-5 |
tables: --tables cds_fpkm input_database: cuffdiff_out.sqlite |
cds_fpkm_output: cds_fpkm.tabular |
cuffdiff_out.sqlite cds_fpkm.tabular |
| Test-6 |
tables: --tables cds_rg input_database: cuffdiff_out.sqlite |
cds_rg_output: cds_rg.tabular |
cuffdiff_out.sqlite cds_rg.tabular |
| Test-7 |
tables: --tables gene_exp_diff input_database: cuffdiff_out.sqlite |
gene_exp_diff_output: gene_exp_diff.tabular |
cuffdiff_out.sqlite gene_exp_diff.tabular |
| Test-8 |
tables: --tables genes_count input_database: cuffdiff_out.sqlite |
genes_count_output: genes_count.tabular |
cuffdiff_out.sqlite genes_count.tabular |
| Test-9 |
tables: --tables genes_fpkm input_database: cuffdiff_out.sqlite |
genes_fpkm_output: genes_fpkm.tabular |
cuffdiff_out.sqlite genes_fpkm.tabular |
| Test-10 |
tables: --tables gene_rg input_database: cuffdiff_out.sqlite |
gene_rg_output: gene_rg.tabular |
cuffdiff_out.sqlite gene_rg.tabular |
| Test-11 |
tables: --tables isoform_exp_diff input_database: cuffdiff_out.sqlite |
isoform_exp_diff_output: isoform_exp_diff.tabular |
cuffdiff_out.sqlite isoform_exp_diff.tabular |
| Test-12 |
tables: --tables isoform_count input_database: cuffdiff_out.sqlite |
isoform_count_output: isoform_count.tabular |
cuffdiff_out.sqlite isoform_count.tabular |
| Test-13 |
tables: --tables isoform_fpkm input_database: cuffdiff_out.sqlite |
isoform_fpkm_output: isoform_fpkm.tabular |
cuffdiff_out.sqlite isoform_fpkm.tabular |
| Test-14 |
tables: --tables isoform_rg input_database: cuffdiff_out.sqlite |
isoform_rg_output: isoform_rg.tabular |
cuffdiff_out.sqlite isoform_rg.tabular |
| Test-15 |
tables: --tables promoters_diff input_database: cuffdiff_out.sqlite |
promoters_diff_output: promoters_diff.tabular |
cuffdiff_out.sqlite promoters_diff.tabular |
| Test-16 |
tables: --tables read_groups input_database: cuffdiff_out.sqlite |
read_groups_output: read_groups.tabular |
cuffdiff_out.sqlite read_groups.tabular |
| Test-17 |
tables: --tables run_info input_database: cuffdiff_out.sqlite |
run_info_output: run_info.tabular |
cuffdiff_out.sqlite run_info.tabular |
| Test-18 |
tables: --tables splicing_diff input_database: cuffdiff_out.sqlite |
splicing_diff_output: splicing_diff.tabular |
cuffdiff_out.sqlite splicing_diff.tabular |
| Test-19 |
tables: --tables tss_group_exp input_database: cuffdiff_out.sqlite |
tss_group_exp_output: tss_group_exp.tabular |
cuffdiff_out.sqlite tss_group_exp.tabular |
| Test-20 |
tables: --tables tss_count_tracking input_database: cuffdiff_out.sqlite |
tss_count_tracking_output: tss_count_tracking.tabular |
cuffdiff_out.sqlite tss_count_tracking.tabular |
| Test-21 |
tables: --tables tss_fpkm input_database: cuffdiff_out.sqlite |
tss_fpkm_output: tss_fpkm.tabular |
cuffdiff_out.sqlite tss_fpkm.tabular |
| Test-22 |
tables: --tables tss_rg input_database: cuffdiff_out.sqlite |
tss_rg_output: tss_rg.tabular |
cuffdiff_out.sqlite tss_rg.tabular |
| Test-23 |
tables: --tables var_model input_database: cuffdiff_out.sqlite |
var_model_output: var_model.tabular |
cuffdiff_out.sqlite var_model.tabular |