| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy0 |
| purge_dups |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| purge_dups | 1.2.5 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
function_select|input: test.paf function_select|coverage: test.cov function_select|cutoffs: cutoffs.tsv function_select|min_bad: 0.01 function_select|min_align: 10 function_select|min_match: 100 function_select|min_chain: 1 function_select|max_gap: 1000 function_select|double_chain|max_gap_2: 1001 function_select|double_chain|chaining_rounds: two function_select|min_chain_score: 1 function_select|max_extend: 100 function_select|functions: purge_dups |
name: value |
test.paf test.cov cutoffs.tsv value |
| Test-2 |
function_select|input: test.paf.gz function_select|coverage: test.cov function_select|cutoffs: cutoffs.tsv function_select|min_bad: 0.01 function_select|min_align: 10 function_select|min_match: 100 function_select|min_chain: 1 function_select|max_gap: 1000 function_select|double_chain|max_gap_2: 1001 function_select|double_chain|chaining_rounds: two function_select|min_chain_score: 1 function_select|max_extend: 100 function_select|functions: purge_dups |
name: value |
test.paf.gz test.cov cutoffs.tsv value |
| Test-3 |
function_select|input: test.fasta function_select|split: True function_select|functions: split_fa |
name: value |
test.fasta value |
| Test-4 |
function_select|input: test.paf function_select|max_cov: 1000 function_select|min_map_ratio: 0.01 function_select|min_map_qual: 1 function_select|flank: 1 function_select|primary_alignments: True function_select|functions: pbcstat |
name: value name: value |
test.paf value |
| Test-5 |
function_select|input: test.paf.gz function_select|max_cov: 1000 function_select|min_map_ratio: 0.01 function_select|min_map_qual: 1 function_select|flank: 1 function_select|primary_alignments: True function_select|functions: pbcstat |
name: value name: value |
test.paf.gz value |
| Test-6 |
function_select|input: test.bam function_select|min_align_qual: 10 function_select|max_insert: 100 function_select|functions: ngscstat |
name: value |
test.bam value |
| Test-7 |
function_select|input: test.stat function_select|min_depth: 0.01 function_select|low_depth: 1 function_select|transition: 1 function_select|upper_depth: 100 function_select|ploidy: -d 0 function_select|functions: calcuts |
name: value |
test.stat value |
| Test-8 |
function_select|fasta_input: split_out.fasta function_select|bed_input: dups.bed function_select|coverage: True function_select|haplotigs: True function_select|length: 10 function_select|min_ratio: .01 function_select|end_trim: True function_select|split: True function_select|min_gap: 100000 function_select|functions: get_seqs |
name: value |
split_out.fasta dups.bed value |