| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.4 |
| toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.3 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.2 |
| toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.1 |
| toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.0 |
| toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/0.0.7 |
| toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/0.0.6 |
| cuffdiff |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| CUFFDIFF_SCRIPT_PATH | not provided | set_environment |
| cufflinks | 2.2.1 | package |
| cummeRbund | 2.8.2 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
bias_correction|do_bias_correction: No gtf_input: cuffdiff_in1.gtf in_type|set_in_type: BAM generate_sqlite: True in_type|conditions_0|name: q1 fdr: 0.05 omit_tabular_output: True additional|sAdditional: No min_alignment_count: 0 in_type|conditions_1|name: q2 multiread_correct: False |
output_cummerbund: cuffdiff_out.sqlite |
cuffdiff_in1.gtf cuffdiff_out.sqlite |
| Test-2 |
bias_correction|do_bias_correction: No gtf_input: cuffdiff_in1.gtf in_type|set_in_type: BAM in_type|conditions_0|name: q1 fdr: 0.05 omit_tabular_output: False additional|sAdditional: No min_alignment_count: 0 in_type|conditions_1|name: q2 multiread_correct: False |
splicing_diff: splicing.diff promoters_diff: promoters.diff cds_diff: cds.diff cds_exp_fpkm_tracking: cds.exp_fpkm_tracking cds_fpkm_tracking: cds.fpkm_tracking tss_groups_exp: tss.groups_exp tss_groups_fpkm_tracking: tss.groups_fpkm_tracking genes_exp: genes.exp genes_fpkm_tracking: genes.fpkm_tracking isoforms_exp: isoforms.exp isoforms_fpkm_tracking: isoforms.fpkm_tracking |
cuffdiff_in1.gtf splicing.diff promoters.diff cds.diff cds.exp_fpkm_tracking cds.fpkm_tracking tss.groups_exp tss.groups_fpkm_tracking genes.exp genes.fpkm_tracking isoforms.exp isoforms.fpkm_tracking |