| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/stacks2_gstacks/stacks2_gstacks/2.55+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/stacks2_gstacks/stacks2_gstacks/2.55+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/stacks2_gstacks/stacks2_gstacks/2.53+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/stacks2_gstacks/stacks2_gstacks/2.4+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/stacks2_gstacks/stacks2_gstacks/2.4+galaxy0 |
| stacks2_gstacks |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| stacks | 2.55 | package |
| python | 3.7 | package |
| findutils | 4.6.0 | package |
| samtools | 1.9 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_bam: ['tsv2bam/PopA_01.matches.bam', 'tsv2bam/PopA_02.matches.bam'] popmap: denovo_map/popmap_cstacks.tsv mode_cond|mode_select: denovo add_log_distribs: True add_log: True |
name: value name: value |
tsv2bam/PopA_01.matches.bam tsv2bam/PopA_02.matches.bam denovo_map/popmap_cstacks.tsv value |
| Test-2 |
input_bam: ['tsv2bam/PopA_01.matches.bam', 'tsv2bam/PopA_02.matches.bam'] popmap: denovo_map/popmap_cstacks.tsv mode_cond|advanced_cond|write_alignments: True mode_cond|advanced_cond|advanced_select: yes mode_cond|mode_select: denovo add_log: True |
name: value |
tsv2bam/PopA_01.matches.bam tsv2bam/PopA_02.matches.bam denovo_map/popmap_cstacks.tsv value |
| Test-3 |
input_bam: tsv2bam/PopA_01.matches.bam mode_cond|ignore_pe_reads: True mode_cond|advanced_cond|kmer_length: 23 mode_cond|advanced_cond|max_debruijn_reads: 666 mode_cond|advanced_cond|min_kmer_cov: 3 mode_cond|advanced_cond|write_alignments: True mode_cond|advanced_cond|advanced_select: yes mode_cond|mode_select: denovo model_cond|var_alpha: 0.1 model_cond|gt_alpha: 0.1 model_cond|model: marukihigh add_log: True |
name: value name: value |
tsv2bam/PopA_01.matches.bam value |
| Test-4 |
input_bam: ['tsv2bam/PopA_01.bam', 'tsv2bam/PopA_02.bam'] mode_cond|paired_cond|rm_pcr_duplicates: True mode_cond|paired_cond|paired_select: mode_cond|mode_select: refbased add_log: True |
tsv2bam/PopA_01.bam tsv2bam/PopA_02.bam |
|
| Test-5 |
input_bam: ['tsv2bam/PopA_01.bam', 'tsv2bam/PopA_02.bam'] popmap: denovo_map/popmap_cstacks.tsv mode_cond|paired_cond|paired_select: --unpaired mode_cond|advanced_cond|min_mapq: 23 mode_cond|advanced_cond|max_clipped: 0.23 mode_cond|advanced_cond|max_insert_len: 666 mode_cond|advanced_cond|details: True mode_cond|advanced_cond|phasing_cooccurrences_thr_min: 2 mode_cond|advanced_cond|phasing_cooccurrences_thr_max: 3 mode_cond|advanced_cond|phasing_dont_prune_hets: True mode_cond|advanced_cond|advanced_select: yes mode_cond|mode_select: refbased model_cond|var_alpha: 0.1 model_cond|gt_alpha: 0.1 model_cond|model: snp add_log: True |
name: value |
tsv2bam/PopA_01.bam tsv2bam/PopA_02.bam denovo_map/popmap_cstacks.tsv value |
| Test-6 |
input_bam: ['tsv2bam/PopA_01.bam', 'tsv2bam/PopA_02.bam'] mode_cond|paired_cond|paired_select: --ignore-pe-reads mode_cond|mode_select: refbased add_log: True |
name: value |
tsv2bam/PopA_01.bam tsv2bam/PopA_02.bam value |