| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/prinseq/prinseq/0.20.4+galaxy2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/prinseq/prinseq/0.20.4+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/prinseq/prinseq/0.20.4 |
| toolshed.g2.bx.psu.edu/repos/iuc/prinseq/prinseq/0.1.0 |
| prinseq |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| prinseq | 0.20.4 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
seq_type|input_singles: prinseq_input_sequences.fastq.gz seq_type|seq_type_opt: single filter_treatments|length_filter_treatments|min_length_filter_treatments|min_length_filter_treatment_value: 60 filter_treatments|length_filter_treatments|min_length_filter_treatments|apply_min_length_filter_treatments: true filter_treatments|length_filter_treatments|max_length_filter_treatments|apply_max_length_filter_treatments: false filter_treatments|length_filter_treatments|apply_length_filter_treatments: true filter_treatments|quality_filter_treatments|min_quality_filter_treatments|apply_min_quality_filter_treatments: false filter_treatments|quality_filter_treatments|max_quality_filter_treatments|apply_max_quality_filter_treatments: false filter_treatments|quality_filter_treatments|mean_quality_filter_treatments|min_mean_quality_filter_treatments|min_mean_quality_filter_treatment_value: 15 filter_treatments|quality_filter_treatments|mean_quality_filter_treatments|min_mean_quality_filter_treatments|apply_min_mean_quality_filter_treatments: true filter_treatments|quality_filter_treatments|mean_quality_filter_treatments|max_mean_quality_filter_treatments|apply_max_mean_quality_filter_treatments: false filter_treatments|quality_filter_treatments|mean_quality_filter_treatments|apply_mean_quality_filter_treatments: true filter_treatments|quality_filter_treatments|apply_quality_filter_treatments: true filter_treatments|base_content_filter_treatments|GC_perc_content_filter_treatments|apply_GC_perc_content_filter_treatments: false filter_treatments|base_content_filter_treatments|N_number_content_filter_treatments|apply_N_number_content_filter_treatments: false filter_treatments|base_content_filter_treatments|N_percentage_content_filter_treatments|N_percentage_content_filter_treatment_value: 2 filter_treatments|base_content_filter_treatments|N_percentage_content_filter_treatments|apply_N_percentage_content_filter_treatments: true filter_treatments|base_content_filter_treatments|apply_other_base_content_filter_treatments: False filter_treatments|base_content_filter_treatments|apply_base_content_filter_treatments: true filter_treatments|complexity_filter_treatments|apply_complexity_filter_treatments: false filter_treatments|apply_filter_treatments: true trimming_treatments|length_trimming_treatments|apply_length_trimming_treatments: false trimming_treatments|position_trimming_treatments|apply_position_trimming_treatments: false trimming_treatments|tail_trimming_treatments|apply_tail_trimming_treatments: false trimming_treatments|quality_trimming_treatments|left_quality_trimming_treatments|apply_left_quality_trimming_treatments: false trimming_treatments|quality_trimming_treatments|right_quality_trimming_treatments|right_quality_trimming_treatment_value: 20 trimming_treatments|quality_trimming_treatments|right_quality_trimming_treatments|apply_right_quality_trimming_treatments: true trimming_treatments|quality_trimming_treatments|type_quality_trimming_treatments: min trimming_treatments|quality_trimming_treatments|rule_quality_trimming_treatments: lt trimming_treatments|quality_trimming_treatments|window_quality_trimming_treatments: 1 trimming_treatments|quality_trimming_treatments|step_quality_trimming_treatments: 1 trimming_treatments|quality_trimming_treatments|apply_quality_trimming_treatments: true trimming_treatments|apply_trimming_treatments: true |
name: value name: value |
prinseq_input_sequences.fastq.gz value |
| Test-2 |
seq_type|input_mate1: pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq seq_type|input_mate2: pairend_strandspecific_51mer_hg19_chr1_1-100000.R2.fastq seq_type|seq_type_opt: paired filter_treatments|length_filter_treatments|min_length_filter_treatments|min_length_filter_treatment_value: 50 filter_treatments|length_filter_treatments|min_length_filter_treatments|apply_min_length_filter_treatments: true filter_treatments|length_filter_treatments|max_length_filter_treatments|apply_max_length_filter_treatments: false filter_treatments|length_filter_treatments|apply_length_filter_treatments: true filter_treatments|quality_filter_treatments|min_quality_filter_treatments|apply_min_quality_filter_treatments: false filter_treatments|quality_filter_treatments|max_quality_filter_treatments|apply_max_quality_filter_treatments: false filter_treatments|quality_filter_treatments|mean_quality_filter_treatments|min_mean_quality_filter_treatments|min_mean_quality_filter_treatment_value: 15 filter_treatments|quality_filter_treatments|mean_quality_filter_treatments|min_mean_quality_filter_treatments|apply_min_mean_quality_filter_treatments: true filter_treatments|quality_filter_treatments|mean_quality_filter_treatments|max_mean_quality_filter_treatments|apply_max_mean_quality_filter_treatments: false filter_treatments|quality_filter_treatments|mean_quality_filter_treatments|apply_mean_quality_filter_treatments: true filter_treatments|quality_filter_treatments|apply_quality_filter_treatments: true filter_treatments|base_content_filter_treatments|GC_perc_content_filter_treatments|apply_GC_perc_content_filter_treatments: false filter_treatments|base_content_filter_treatments|N_number_content_filter_treatments|apply_N_number_content_filter_treatments: false filter_treatments|base_content_filter_treatments|N_percentage_content_filter_treatments|N_percentage_content_filter_treatment_value: 2 filter_treatments|base_content_filter_treatments|N_percentage_content_filter_treatments|apply_N_percentage_content_filter_treatments: true filter_treatments|base_content_filter_treatments|apply_other_base_content_filter_treatments: False filter_treatments|base_content_filter_treatments|apply_base_content_filter_treatments: true filter_treatments|complexity_filter_treatments|apply_complexity_filter_treatments: false filter_treatments|apply_filter_treatments: true trimming_treatments|length_trimming_treatments|apply_length_trimming_treatments: false trimming_treatments|position_trimming_treatments|apply_position_trimming_treatments: false trimming_treatments|tail_trimming_treatments|apply_tail_trimming_treatments: false trimming_treatments|quality_trimming_treatments|left_quality_trimming_treatments|apply_left_quality_trimming_treatments: false trimming_treatments|quality_trimming_treatments|right_quality_trimming_treatments|right_quality_trimming_treatment_value: 20 trimming_treatments|quality_trimming_treatments|right_quality_trimming_treatments|apply_right_quality_trimming_treatments: true trimming_treatments|quality_trimming_treatments|type_quality_trimming_treatments: min trimming_treatments|quality_trimming_treatments|rule_quality_trimming_treatments: lt trimming_treatments|quality_trimming_treatments|window_quality_trimming_treatments: 1 trimming_treatments|quality_trimming_treatments|step_quality_trimming_treatments: 1 trimming_treatments|quality_trimming_treatments|apply_quality_trimming_treatments: true trimming_treatments|apply_trimming_treatments: true |
name: value name: value name: value name: value name: value name: value |
pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq pairend_strandspecific_51mer_hg19_chr1_1-100000.R2.fastq value |
| Test-3 |
seq_type|input_collection: paired collection seq_type|seq_type_opt: paired_collection filter_treatments|length_filter_treatments|min_length_filter_treatments|min_length_filter_treatment_value: 50 filter_treatments|length_filter_treatments|min_length_filter_treatments|apply_min_length_filter_treatments: true filter_treatments|length_filter_treatments|max_length_filter_treatments|apply_max_length_filter_treatments: false filter_treatments|length_filter_treatments|apply_length_filter_treatments: true filter_treatments|quality_filter_treatments|min_quality_filter_treatments|apply_min_quality_filter_treatments: false filter_treatments|quality_filter_treatments|max_quality_filter_treatments|apply_max_quality_filter_treatments: false filter_treatments|quality_filter_treatments|mean_quality_filter_treatments|min_mean_quality_filter_treatments|min_mean_quality_filter_treatment_value: 15 filter_treatments|quality_filter_treatments|mean_quality_filter_treatments|min_mean_quality_filter_treatments|apply_min_mean_quality_filter_treatments: true filter_treatments|quality_filter_treatments|mean_quality_filter_treatments|max_mean_quality_filter_treatments|apply_max_mean_quality_filter_treatments: false filter_treatments|quality_filter_treatments|mean_quality_filter_treatments|apply_mean_quality_filter_treatments: true filter_treatments|quality_filter_treatments|apply_quality_filter_treatments: true filter_treatments|base_content_filter_treatments|GC_perc_content_filter_treatments|apply_GC_perc_content_filter_treatments: false filter_treatments|base_content_filter_treatments|N_number_content_filter_treatments|apply_N_number_content_filter_treatments: false filter_treatments|base_content_filter_treatments|N_percentage_content_filter_treatments|N_percentage_content_filter_treatment_value: 2 filter_treatments|base_content_filter_treatments|N_percentage_content_filter_treatments|apply_N_percentage_content_filter_treatments: true filter_treatments|base_content_filter_treatments|apply_other_base_content_filter_treatments: False filter_treatments|base_content_filter_treatments|apply_base_content_filter_treatments: true filter_treatments|complexity_filter_treatments|apply_complexity_filter_treatments: false filter_treatments|apply_filter_treatments: true trimming_treatments|length_trimming_treatments|apply_length_trimming_treatments: false trimming_treatments|position_trimming_treatments|apply_position_trimming_treatments: false trimming_treatments|tail_trimming_treatments|apply_tail_trimming_treatments: false trimming_treatments|quality_trimming_treatments|left_quality_trimming_treatments|apply_left_quality_trimming_treatments: false trimming_treatments|quality_trimming_treatments|right_quality_trimming_treatments|right_quality_trimming_treatment_value: 20 trimming_treatments|quality_trimming_treatments|right_quality_trimming_treatments|apply_right_quality_trimming_treatments: true trimming_treatments|quality_trimming_treatments|type_quality_trimming_treatments: min trimming_treatments|quality_trimming_treatments|rule_quality_trimming_treatments: lt trimming_treatments|quality_trimming_treatments|window_quality_trimming_treatments: 1 trimming_treatments|quality_trimming_treatments|step_quality_trimming_treatments: 1 trimming_treatments|quality_trimming_treatments|apply_quality_trimming_treatments: true trimming_treatments|apply_trimming_treatments: true |
pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq.gz pairend_strandspecific_51mer_hg19_chr1_1-100000.R2.fastq.gz |