| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.6 |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.5 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4 |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.3 |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.1 |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1 |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.0 |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.3 |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.2 |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.1 |
| samtools_mpileup |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| samtools | 1.13 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input: ['mpileup.1.bam', 'mpileup.2.bam', 'mpileup.3.bam'] addref_cond|ref: mpileup.ref.fa addref_cond|addref_select: history advanced_options|limit_by_region|region_paste: 17:100-150 advanced_options|limit_by_region|limit_by_regions: limit advanced_options|advanced_options_selector: advanced |
name: value |
mpileup.1.bam mpileup.2.bam mpileup.3.bam mpileup.ref.fa value |
| Test-2 |
input: mpileup.1.bam addref_cond|ref: mpileup.ref.fa addref_cond|addref_select: history advanced_options|filter_by_flags|exclude_flags: ['4', '16'] advanced_options|filter_by_flags|filter_flags: filter advanced_options|limit_by_region|region_paste: 17:1050-1060 advanced_options|limit_by_region|limit_by_regions: limit advanced_options|disable_probabilistic_realignment: True advanced_options|advanced_options_selector: advanced |
name: value |
mpileup.1.bam mpileup.ref.fa value |
| Test-3 |
input: samtools_mpileup_in_1.bam addref_cond|ref: phiX.fasta addref_cond|addref_select: history advanced_options|advanced_options_selector: default output_options_cond|base_position_on_reads: True output_options_cond|output_mapping_quality: True output_options_cond|output_options_selector: advanced |
name: value |
samtools_mpileup_in_1.bam phiX.fasta value |
| Test-4 |
input: phiX.bam addref_cond|ref: phiX.fasta addref_cond|addref_select: history advanced_options|skip_anomalous_read_pairs: True advanced_options|advanced_options_selector: advanced output_options_cond|output_options_selector: default |
name: value |
phiX.bam phiX.fasta value |
| Test-5 |
input: samtools_mpileup_in_1.bam addref_cond|ref: phiX.fasta addref_cond|addref_select: history advanced_options|minimum_base_quality: 0 advanced_options|advanced_options_selector: advanced output_options_cond|base_position_on_reads: True output_options_cond|output_mapping_quality: True output_options_cond|output_options_selector: advanced |
name: value |
samtools_mpileup_in_1.bam phiX.fasta value |
| Test-6 |
input: mpileup.1.bam addref_cond|ref: mpileup.ref.fa addref_cond|addref_select: history output_options_cond|output_tags: NM,AM output_options_cond|output_options_selector: advanced |
name: value |
mpileup.1.bam mpileup.ref.fa value |