| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/4.3.6+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.6 (this tool) |
| toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.5 |
| toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.4 |
| toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.3 |
| toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.2 |
| toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.1 |
| toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.0 |
| toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.0.0 |
| bg_sortmerna |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| sortmerna | 2.1b | package |
| samtools | 1.5 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
strand_search: report|print_all_reads: False log: False report|blast|blast_output: True databases_type|database_name: ref_small.fasta sequencing_type|reads: read_small.fastq mismatch: -3 ambiguous_letter: -3 databases_type|databases_selector: history aligned_fastx|aligned_fastx_selector: --fastx report|blast|blast_format: 1 cigar qcov aligned_fastx|other: True gap_open: 5 sequencing_type|sequencing_type_selector: not_paired e_value: 1 report|report_type: num_alignments match: 2 gap_ext: 2 |
attributes: name attributes: name attributes: name attributes: name |
read_small.fastq ref_small.fasta name |
| Test-2 |
log: True databases_type|database_name: ref_small.fasta sequencing_type|reads: read_small.fasta mismatch: -3 ambiguous_letter: -3 databases_type|databases_selector: history aligned_fastx|aligned_fastx_selector: --fastx match: 2 aligned_fastx|other: False gap_open: 5 sequencing_type|sequencing_type_selector: not_paired e_value: 1 report|report_type: None strand_search: gap_ext: 2 |
attributes: name attributes: name |
read_small.fasta ref_small.fasta name |
| Test-3 |
report|blast|blast_output: False ambiguous_letter: -3 databases_type|databases_selector: history sequencing_type|forward_reads: forward_reads.fastq strand_search: log: False e_value: 1 match: 2 gap_ext: 2 databases_type|database_name: ref_small.fasta mismatch: -3 aligned_fastx|aligned_fastx_selector: --fastx report|report_type: best aligned_fastx|other: True report|print_all_reads: False sequencing_type|reverse_reads: reverse_reads.fastq databases_type|seed_length: 18 gap_open: 5 sequencing_type|sequencing_type_selector: paired databases_type|max_pos: 100000 sequencing_type|paired_type: --paired_in report|otu|otu_map: False |
attributes: name attributes: name attributes: name attributes: name attributes: name |
forward_reads.fastq reverse_reads.fastq ref_small.fasta name |
| Test-4 |
report|blast|blast_output: False ambiguous_letter: -3 databases_type|databases_selector: history strand_search: log: False e_value: 1 match: 2 gap_ext: 2 sequencing_type|reads: test4_input.fasta report|otu|de_novo_otu: True databases_type|database_name: ref_small.fasta mismatch: -3 aligned_fastx|aligned_fastx_selector: report|otu|id: 0.97 report|report_type: best report|otu|coverage: 0.97 report|print_all_reads: False databases_type|seed_length: 18 gap_open: 5 sequencing_type|sequencing_type_selector: not_paired databases_type|max_pos: 100000 report|otu|otu_map: True |
attributes: name attributes: name attributes: name |
test4_input.fasta ref_small.fasta name |
| Test-5 |
report|blast|blast_output: False ambiguous_letter: -3 databases_type|databases_selector: history sequencing_type|forward_reads: forward_reads.fasta strand_search: log: False e_value: 1 match: 2 gap_ext: 2 databases_type|database_name: ref_small.fasta mismatch: -3 aligned_fastx|aligned_fastx_selector: --fastx report|report_type: best aligned_fastx|other: True report|print_all_reads: False sequencing_type|reverse_reads: reverse_reads.fasta databases_type|seed_length: 18 gap_open: 5 sequencing_type|sequencing_type_selector: paired databases_type|max_pos: 100000 sequencing_type|paired_type: report|otu|otu_map: False |
attributes: name attributes: name |
forward_reads.fasta reverse_reads.fasta ref_small.fasta name |
| Test-6 |
report|blast|blast_output: False ambiguous_letter: -3 databases_type|databases_selector: history sequencing_type|forward_reads: forward_reads.fasta strand_search: log: False e_value: 1 match: 2 gap_ext: 2 databases_type|database_name: ref_small.fasta mismatch: -3 aligned_fastx|aligned_fastx_selector: --fastx report|report_type: best aligned_fastx|other: True report|print_all_reads: False sequencing_type|reverse_reads: reverse_reads.fasta databases_type|seed_length: 18 gap_open: 5 sequencing_type|sequencing_type_selector: paired databases_type|max_pos: 100000 sequencing_type|paired_type: --paired_out report|otu|otu_map: False |
attributes: name attributes: name attributes: name attributes: name |
forward_reads.fasta reverse_reads.fasta ref_small.fasta name |