| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/polypolish/polypolish/0.5.0+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/polypolish/polypolish/0.5.0+galaxy0 (this tool) |
| polypolish |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| polypolish | 0.5.0 | package |
| samtools | 1.13 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input|fasta_file: contigs.fa input|sam_data_type|single_sam: aligned_test_file/alignement_R1.sam input|sam_data_type|sam_selector: single |
name: value |
contigs.fa aligned_test_file/alignement_R1.sam value |
| Test-2 |
input|fasta_file: contigs.fa input|sam_data_type|R1_sam: aligned_test_file/alignement_R1.sam input|sam_data_type|R2_sam: aligned_test_file/alignement_R2.sam input|sam_data_type|sam_selector: paired options|keep_logfile: False options|debug: True |
name: value name: value |
contigs.fa aligned_test_file/alignement_R1.sam aligned_test_file/alignement_R2.sam value |
| Test-3 |
input|fasta_file: contigs.fa input|sam_data_type|single_collection: list collection input|sam_data_type|sam_selector: multiple_single options|keep_logfile: True options|debug: False |
name: value name: value |
contigs.fa aligned_test_file/alignement_R1.sam aligned_test_file/alignement_R1_bis.sam aligned_test_file/alignement_R1_ter.sam value |
| Test-4 |
input|fasta_file: contigs.fa input|sam_data_type|paired_collection: list:paired collection input|sam_data_type|sam_selector: multiple_paired |
name: value |
contigs.fa aligned_test_file/alignement_R1.sam aligned_test_file/alignement_R2.sam aligned_test_file/alignement_R1_bis.sam aligned_test_file/alignement_R2_bis.sam aligned_test_file/alignement_R1_ter.sam aligned_test_file/alignement_R2_ter.sam value |
| Test-5 |
input|fasta_file: contigs.fa input|sam_data_type|R1_sam: aligned_test_file/alignement_R1.sam input|sam_data_type|R2_sam: aligned_test_file/alignement_R2.sam input|sam_data_type|sam_selector: paired options|keep_logfile: False options|debug: False |
name: value |
contigs.fa aligned_test_file/alignement_R1.sam aligned_test_file/alignement_R2.sam value |
| Test-6 |
input|fasta_file: contigs.fa input|sam_data_type|R1_sam: aligned_test_file/alignement_R1.sam input|sam_data_type|R2_sam: aligned_test_file/alignement_R2.sam input|sam_data_type|insert_filter|low: 1 input|sam_data_type|insert_filter|high: 98.7 input|sam_data_type|insert_filter|filter_select: filter input|sam_data_type|sam_selector: paired options|keep_logfile: False options|debug: False |
name: value |
contigs.fa aligned_test_file/alignement_R1.sam aligned_test_file/alignement_R2.sam value |
| Test-7 |
input|fasta_file: contigs.fa input|sam_data_type|R1_sam: aligned_test_file/alignement_R1.sam input|sam_data_type|R2_sam: aligned_test_file/alignement_R2.sam input|sam_data_type|insert_filter|low: 1.4 input|sam_data_type|insert_filter|high: 96.6 input|sam_data_type|insert_filter|filter_select: filter input|sam_data_type|sam_selector: paired options|min_depth: 10 options|fraction_invalid: 0.5 options|max_errors: 8 options|fraction_valid: 0.6 options|keep_logfile: False options|debug: False |
name: value |
contigs.fa aligned_test_file/alignement_R1.sam aligned_test_file/alignement_R2.sam value |
| Test-8 |
input|fasta_file: contigs.fa input|sam_data_type|single_sam: aligned_test_file/alignement_R1.bam input|sam_data_type|sam_selector: single options|keep_logfile: False options|debug: False |
name: value |
contigs.fa aligned_test_file/alignement_R1.bam value |
| Test-9 |
input|fasta_file: contigs.fa input|sam_data_type|R1_sam: aligned_test_file/alignement_R1.bam input|sam_data_type|R2_sam: aligned_test_file/alignement_R2.bam input|sam_data_type|sam_selector: paired options|keep_logfile: False options|debug: False |
name: value |
contigs.fa aligned_test_file/alignement_R1.bam aligned_test_file/alignement_R2.bam value |
| Test-10 |
input|fasta_file: contigs.fa input|sam_data_type|single_collection: list collection input|sam_data_type|sam_selector: multiple_single options|keep_logfile: False options|debug: False |
name: value |
contigs.fa aligned_test_file/alignement_R1.bam aligned_test_file/alignement_R1_bis.bam aligned_test_file/alignement_R1_ter.bam value |
| Test-11 |
input|fasta_file: contigs.fa input|sam_data_type|paired_collection: list:paired collection input|sam_data_type|sam_selector: multiple_paired options|keep_logfile: False options|debug: False |
name: value |
contigs.fa aligned_test_file/alignement_R1.bam aligned_test_file/alignement_R2.bam aligned_test_file/alignement_R1_bis.bam aligned_test_file/alignement_R2_bis.bam aligned_test_file/alignement_R1_ter.bam aligned_test_file/alignement_R2_ter.bam value |