| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/thondeboer/neat_genreads/neat_genreads/1.0.0 (this tool) |
| neat_genreads |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| numpy | not provided | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
out_options|golden_vcf: False read_length: 101 out_options|golden_bam: False out_options|prefix: out in_type|input_type: history stats|seed: 1 in_type|reference: chrMT.fa lib_type_cond|lib_type: single out_options|compress: False |
attributes: name |
chrMT.fa name |
| Test-2 |
lib_type_cond|insert_mod_cond|insert_mod: fixed_insert out_options|golden_vcf: False out_options|golden_bam: False read_length: 101 lib_type_cond|insert_mod_cond|frag_length_sd: 30 out_options|prefix: out in_type|input_type: history stats|seed: 1 in_type|reference: chrMT.fa lib_type_cond|lib_type: paired lib_type_cond|insert_mod_cond|frag_length: 300 out_options|compress: False |
attributes: name attributes: name |
chrMT.fa name |
| Test-3 |
lib_type_cond|insert_mod_cond|insert_mod: fixed_insert out_options|golden_vcf: True out_options|golden_bam: True read_length: 101 lib_type_cond|insert_mod_cond|frag_length_sd: 30 out_options|prefix: out in_type|input_type: history stats|seed: 1 in_type|reference: chrMT.fa lib_type_cond|lib_type: paired lib_type_cond|insert_mod_cond|frag_length: 300 out_options|compress: False |
attributes: name attributes: name attributes: name attributes: name |
chrMT.fa name |
| Test-4 |
lib_type_cond|insert_mod_cond|insert_mod: fixed_insert out_options|golden_vcf: True out_options|golden_bam: True read_length: 101 target_vcf_cond|target_vcf: use_vcf lib_type_cond|insert_mod_cond|frag_length_sd: 30 out_options|prefix: out in_type|input_type: history stats|seed: 1 target_vcf_cond|target_file: chrMT-PE-VCF-BAM.vcf in_type|reference: chrMT.fa lib_type_cond|lib_type: paired lib_type_cond|insert_mod_cond|frag_length: 300 out_options|compress: False |
attributes: name attributes: name attributes: name attributes: name |
chrMT.fa chrMT-PE-VCF-BAM.vcf name |
| Test-5 |
lib_type_cond|insert_mod_cond|insert_mod: fixed_insert out_options|golden_vcf: True lib_type_cond|insert_mod_cond|frag_length_sd: 30 read_length: 101 target_cond|off_target: 0.02 target_cond|target_file: chrMT-Targets.bed out_options|golden_bam: True out_options|prefix: out in_type|input_type: history stats|seed: 1 in_type|reference: chrMT.fa lib_type_cond|lib_type: paired lib_type_cond|insert_mod_cond|frag_length: 300 out_options|compress: False target_cond|target: targeted |
attributes: name attributes: name attributes: name attributes: name |
chrMT.fa chrMT-Targets.bed name |
| Test-6 |
lib_type_cond|insert_mod_cond|insert_mod: fixed_insert out_options|golden_vcf: True out_options|golden_bam: True read_length: 101 lib_type_cond|insert_mod_cond|frag_length_sd: 30 out_options|prefix: out in_type|input_type: history stats|seed: 1 in_type|reference: chrMT.fa lib_type_cond|lib_type: paired lib_type_cond|insert_mod_cond|frag_length: 300 out_options|compress: True |
attributes: name attributes: name |
chrMT.fa name |
| Test-7 |
lib_type_cond|insert_mod_cond|insert_mod: fixed_insert out_options|golden_vcf: True stats|mut_rate_cond|error_rate: 0.123 coverage: 20 lib_type_cond|insert_mod_cond|frag_length_sd: 50 read_length: 151 stats|error_model_cond|error_rate: 0.123 out_options|golden_bam: True stats|ploidy: 3 out_options|prefix: out stats|error_model_cond|error_model: average_rate stats|mut_rate_cond|mut_rate: average_rate stats|seed: 123 in_type|reference: chrMT.fa lib_type_cond|lib_type: paired lib_type_cond|insert_mod_cond|frag_length: 500 out_options|compress: False in_type|input_type: history |
attributes: name attributes: name attributes: name attributes: name |
chrMT.fa name |
| Test-8 |
out_options|golden_vcf: False read_length: 101 out_options|golden_bam: False out_options|prefix: out in_type|input_type: built-in stats|seed: 1 in_type|reference: hg19chrmt lib_type_cond|lib_type: single out_options|compress: False |
attributes: name |
name |