| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/amplican/amplican/1.14.0+galaxy0 (this tool) |
| amplican |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bioconductor-amplican | 1.14.0 | package |
| Additional information about this tool |
#import re
mkdir ./fastq_folder ./output_folder
#for $i in $fastq_files
#if str($i.element_identifier) != re.sub('[^\w\-_\.]', '_', str($i.element_identifier))
&& echo "Please rename your datasets; only underscore (_) and alphanumeric characters are allowed."
&& exit 1
#else
&& ln -s '${i}' ./fastq_folder/'${i.element_identifier}'
#end if
#end for
&& Rscript '$amplican_script'
#if 'knit_reports' in $output_options.outputs
&& mv ./output_folder/reports/amplicon_report.html '${output_html.extra_files_path}'
&& mv ./output_folder/reports/barcode_report.html '${output_html.extra_files_path}'
&& mv ./output_folder/reports/group_report.html '${output_html.extra_files_path}'
&& mv ./output_folder/reports/guide_report.html '${output_html.extra_files_path}'
&& mv ./output_folder/reports/id_report.html '${output_html.extra_files_path}'
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
config_file: config.csv fastq_files: ['R1_001.fastq', 'R1_002.fastq', 'R2_001.fastq', 'R2_002.fastq'] quality_options|average_quality: 0 quality_options|min_quality: 20 alignment_options|gap_opening: 25 alignment_options|gap_extension: 0 alignment_options|primer_mismatch: 0 alignment_options|donor_mismatch: 3 alignment_options|scoring_matrix|match_scoring: 5 alignment_options|scoring_matrix|base_only: True alignment_options|scoring_matrix|scoring_type: DNA advanced_options|fastq_use: 0 advanced_options|primer_dimer: 30 advanced_options|event_filter: True advanced_options|cut_buffer: 5 advanced_options|promiscuous_consensus: True output_options|write_alignment_format: txt output_options|outputs: ['config_summary', 'barcode_reads', 'knit_reports', 'parameters', 'alignments_rds', 'events_filtered_shifted', 'events_filtered_shifted_normalized', 'raw_events', 'unassigned_reads'] |
name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value |
config.csv R1_001.fastq R1_002.fastq R2_001.fastq R2_002.fastq value |
| Test-2 |
config_file: config.csv fastq_files: ['R1_001.fastq', 'R1_002.fastq', 'R2_001.fastq', 'R2_002.fastq'] quality_options|average_quality: 0 quality_options|min_quality: 20 alignment_options|gap_opening: 25 alignment_options|gap_extension: 0 alignment_options|primer_mismatch: 0 alignment_options|donor_mismatch: 3 alignment_options|scoring_matrix|match_scoring: 5 alignment_options|scoring_matrix|base_only: True alignment_options|scoring_matrix|scoring_type: DNA advanced_options|fastq_use: 0 advanced_options|primer_dimer: 30 advanced_options|event_filter: True advanced_options|cut_buffer: 5 advanced_options|promiscuous_consensus: True output_options|write_alignment_format: fasta output_options|outputs: ['config_summary', 'barcode_reads', 'knit_reports', 'parameters', 'alignments_rds', 'events_filtered_shifted', 'events_filtered_shifted_normalized', 'raw_events', 'unassigned_reads'] |
name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value |
config.csv R1_001.fastq R1_002.fastq R2_001.fastq R2_002.fastq value |
| Test-3 |
config_file: config.csv fastq_files: ['R1_001.fastq', 'R1_002.fastq', 'R2_001.fastq', 'R2_002.fastq'] quality_options|average_quality: 0 quality_options|min_quality: 20 alignment_options|gap_opening: 25 alignment_options|gap_extension: 0 alignment_options|primer_mismatch: 0 alignment_options|donor_mismatch: 3 alignment_options|scoring_matrix|match_scoring: 5 alignment_options|scoring_matrix|base_only: True alignment_options|scoring_matrix|scoring_type: DNA advanced_options|fastq_use: 0 advanced_options|primer_dimer: 30 advanced_options|event_filter: True advanced_options|cut_buffer: 5 advanced_options|promiscuous_consensus: True output_options|write_alignment_format: fasta output_options|outputs: config_summary |
name: value name: value |
config.csv R1_001.fastq R1_002.fastq R2_001.fastq R2_002.fastq value |
| Test-4 |
config_file: config_gzip.csv fastq_files: ['R1_001.fastq.gz', 'R1_002.fastq.gz', 'R2_001.fastq.gz', 'R2_002.fastq.gz'] output_options|write_alignment_format: fasta output_options|outputs: config_summary |
name: value name: value |
config_gzip.csv R1_001.fastq.gz R1_002.fastq.gz R2_001.fastq.gz R2_002.fastq.gz value |