| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/pjbriggs/pal_finder/microsat_pal_finder/0.02.04.8 (this tool) |
| toolshed.g2.bx.psu.edu/repos/pjbriggs/pal_finder/microsat_pal_finder/0.02.04.7 |
| toolshed.g2.bx.psu.edu/repos/pjbriggs/pal_finder/microsat_pal_finder/0.02.04.6 |
| toolshed.g2.bx.psu.edu/repos/pjbriggs/pal_finder/microsat_pal_finder/0.02.04.5 |
| toolshed.g2.bx.psu.edu/repos/pjbriggs/pal_finder/microsat_pal_finder/0.02.04.4 |
| toolshed.g2.bx.psu.edu/repos/pjbriggs/pal_finder/microsat_pal_finder/0.02.04.3 |
| toolshed.g2.bx.psu.edu/repos/pjbriggs/pal_finder/microsat_pal_finder/0.02.04.2 |
| toolshed.g2.bx.psu.edu/repos/pjbriggs/pal_finder/microsat_pal_finder/0.02.04.1 |
| microsat_pal_finder |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| pal_finder | 0.02.04 | package |
| python | 2.7 | package |
| biopython | 1.65 | package |
| pandaseq | 2.8.1 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
platform|paired_input_type_conditional|input_fastq_r1: illuminaPE_r1.fq platform|paired_input_type_conditional|input_fastq_r2: illuminaPE_r2.fq platform|platform_type: illumina |
attributes: name attributes: name attributes: name attributes: name |
illuminaPE_r1.fq illuminaPE_r2.fq name |
| Test-2 |
platform|paired_input_type_conditional|paired_input_type: collection platform|platform_type: illumina platform|paired_input_type_conditional|input_fastq_pair: paired collection |
attributes: name attributes: name attributes: name attributes: name |
illuminaPE_r1.fq illuminaPE_r2.fq name |
| Test-3 |
platform|paired_input_type_conditional|input_fastq_r1: illuminaPE_r1.fq platform|paired_input_type_conditional|input_fastq_r2: illuminaPE_r2.fq platform|filters: platform|platform_type: illumina |
attributes: name attributes: name attributes: name |
illuminaPE_r1.fq illuminaPE_r2.fq name |
| Test-4 |
platform|paired_input_type_conditional|input_fastq_r1: illuminaPE_r1.fq platform|paired_input_type_conditional|input_fastq_r2: illuminaPE_r2.fq platform|filters: -primers platform|assembly: False platform|platform_type: illumina |
attributes: name attributes: name attributes: name |
illuminaPE_r1.fq illuminaPE_r2.fq name |
| Test-5 |
platform|paired_input_type_conditional|input_fastq_r1: illuminaPE_r1.fq platform|paired_input_type_conditional|input_fastq_r2: illuminaPE_r2.fq platform|filters: -occurrences platform|assembly: False platform|platform_type: illumina |
attributes: name attributes: name attributes: name |
illuminaPE_r1.fq illuminaPE_r2.fq name |
| Test-6 |
platform|paired_input_type_conditional|input_fastq_r1: illuminaPE_r1.fq platform|paired_input_type_conditional|input_fastq_r2: illuminaPE_r2.fq platform|filters: -rankmotifs platform|assembly: False platform|platform_type: illumina |
attributes: name attributes: name attributes: name |
illuminaPE_r1.fq illuminaPE_r2.fq name |
| Test-7 |
platform|platform_type: illumina platform|filters: platform|subset_conditional|use_all_reads: False platform|subset_conditional|subset: 0.5 platform|assembly: False platform|paired_input_type_conditional|input_fastq_r1: illuminaPE_r1.fq platform|paired_input_type_conditional|input_fastq_r2: illuminaPE_r2.fq |
attributes: name attributes: name |
illuminaPE_r1.fq illuminaPE_r2.fq name |
| Test-8 |
platform|platform_type: illumina platform|filters: platform|paired_input_type_conditional|input_fastq_r1: illuminaPE_r1_no_microsats.fq platform|assembly: False min_2mer_repeats: 8 platform|paired_input_type_conditional|input_fastq_r2: illuminaPE_r2_no_microsats.fq |
illuminaPE_r1_no_microsats.fq illuminaPE_r2_no_microsats.fq |
|
| Test-9 |
min_3mer_repeats: 8 min_6mer_repeats: 8 platform|assembly: False primer|primer_min_tm: 60.0 primer|primer_opt_size: 25 primer|primer_gc_clamp: 3 primer|primer_min_gc: 40.0 primer|primer_max_gc: 60.0 primer|primer_max_tm: 80.0 platform|paired_input_type_conditional|input_fastq_r1: illuminaPE_r1_bad_ranges.fq platform|paired_input_type_conditional|input_fastq_r2: illuminaPE_r2_bad_ranges.fq primer|primer_max_end_gc: 5 primer|primer_pair_max_diff_tm: 3.0 platform|platform_type: illumina primer|primer_options: custom min_5mer_repeats: 8 platform|filters: primer|primer_opt_tm: 68.0 primer|primer_min_size: 21 min_2mer_repeats: 8 report_bad_primer_ranges: True primer|primer_max_size: 30 min_4mer_repeats: 8 |
attributes: name attributes: name attributes: name |
illuminaPE_r1_bad_ranges.fq illuminaPE_r2_bad_ranges.fq name |
| Test-10 |
platform|platform_type: illumina min_6mer_repeats: 8 platform|paired_input_type_conditional|input_fastq_r1: illuminaPE_r1_no_microsats.fq min_3mer_repeats: 8 platform|assembly: False min_5mer_repeats: 8 min_2mer_repeats: 8 platform|filters: platform|paired_input_type_conditional|input_fastq_r2: illuminaPE_r2_no_microsats.fq min_4mer_repeats: 0 |
illuminaPE_r1_no_microsats.fq illuminaPE_r2_no_microsats.fq |
|
| Test-11 |
platform|platform_type: 454 platform|input_fasta: 454_in.fa |
attributes: name attributes: name |
454_in.fa name |