| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_mapping/seq_filter_by_mapping/0.0.8 (this tool) |
| toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_mapping/seq_filter_by_mapping/0.0.7 |
| toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_mapping/seq_filter_by_mapping/0.0.6 |
| toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_mapping/seq_filter_by_mapping/0.0.5 |
| toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_mapping/seq_filter_by_mapping/0.0.4 |
| toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_mapping/seq_filter_by_mapping/0.0.2 |
| seq_filter_by_mapping |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| biopython | 1.81 | package |
| samtools | 0.1.19 | package |
| Additional information about this tool |
python $__tool_directory__/seq_filter_by_mapping.py -i '$input_file' -f '$input_file.ext' -m $pair_mode
#if $output_choice_cond.output_choice=="both"
-p '$output_pos' -n '$output_neg'
#elif $output_choice_cond.output_choice=="pos"
-p '$output_pos'
#elif $output_choice_cond.output_choice=="neg"
-n '$output_neg'
#end if
## Now loop over all the mapping files
#for i in $mapping_file#'${i}' #end for#
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_file: SRR639755_mito_pairs.fastq.gz mapping_file: SRR639755_sample_by_coord.sam output_choice_cond|output_choice: pos pair_mode: lax |
name: value |
SRR639755_mito_pairs.fastq.gz SRR639755_sample_by_coord.sam value |
| Test-2 |
input_file: SRR639755_mito_pairs.fastq.gz mapping_file: SRR639755_sample_by_coord.sam output_choice_cond|output_choice: pos pair_mode: strict |
name: value |
SRR639755_mito_pairs.fastq.gz SRR639755_sample_by_coord.sam value |