| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.1 |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1 (this tool) |
| 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 | 1.2 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
genotype_likelihood_computation_type|base_position_on_reads: True reference_source|reference_source_selector: history genotype_likelihood_computation_type|genotype_likelihood_computation_type_selector: do_not_perform_genotype_likelihood_computation advanced_options|advanced_options_selector: basic reference_source|input_bams_0|input_bam: samtools_mpileup_in_1.bam reference_source|ref_file: phiX.fasta genotype_likelihood_computation_type|output_mapping_quality: True |
output_mpileup: samtools_mpileup_out_1.pileup output_log: samtools_mpileup_out_1.log |
samtools_mpileup_in_1.bam phiX.fasta samtools_mpileup_out_1.pileup samtools_mpileup_out_1.log |
| Test-2 |
genotype_likelihood_computation_type|genotype_likelihood_computation_type_selector: perform_genotype_likelihood_computation genotype_likelihood_computation_type|perform_indel_calling|coefficient_for_modeling_homopolymer_errors: 100 reference_source|reference_source_selector: history genotype_likelihood_computation_type|perform_indel_calling|gap_open_sequencing_error_probability: 40 genotype_likelihood_computation_type|perform_indel_calling|perform_indel_calling_selector: perform_indel_calling genotype_likelihood_computation_type|perform_indel_calling|skip_indel_calling_above_sample_depth: 250 genotype_likelihood_computation_type|output_format: --VCF advanced_options|advanced_options_selector: basic reference_source|input_bams_0|input_bam: phiX.bam genotype_likelihood_computation_type|perform_indel_calling|gap_extension_sequencing_error_probability: 20 reference_source|ref_file: phiX.fasta |
output_mpileup: samtools_mpileup_out_2.vcf output_log: samtools_mpileup_out_2.log |
phiX.bam phiX.fasta samtools_mpileup_out_2.vcf samtools_mpileup_out_2.log |