| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/nonpareil/nonpareil/3.5.5+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/nonpareil/nonpareil/3.5.5+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/nonpareil/nonpareil/3.1.1.1 |
| toolshed.g2.bx.psu.edu/repos/iuc/nonpareil/nonpareil/3.1.1.0 |
| nonpareil |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| nonpareil | 3.5.5 | package |
| Additional information about this tool |
#import re
#set summary_path = re.sub('[^\s\w\-.]', '_', str($input.element_identifier))
ln -s '$input' input &&
nonpareil
-s input
-T '$algo'
#if $input.is_of_type("fasta")
-f 'fasta'
#else if $input.is_of_type("fastq")
-f 'fastq'
#end if
-d '$subsampling'
-n '$subsample_per_point'
-L '$min_overlapping'
-X '$max_query_reads'
-R \${NONPAREIL_MAX_MEMORY:-1024}
-t \${GALAXY_SLOTS:-2}
-b output
-a '$all_data_output'
-C '$mating_vector_output'
#if $log_test
-l '$log'
#end if
-o '$summary_path'
$use_portion_in_output
-m '$sampling.min_sampling_portion'
-M '$sampling.max_sampling_portion'
-i '$sampling.sampling_portion_interval'
$mating.use_rev_comp
$mating.n_as_mismatches
#if str($mating.sim_thres) != ''
-S '$mating.sim_thres'
#end if
-k '$mating.kmer_size'
#if str($mating.proba) != ''
-x '$mating.proba'
#end if
-r '$seed'
&& cp '$summary_path' '$summary'
#if '$json_object'
&& NonpareilCurves.R --json '$json_output' '$summary_path'
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input: test.fasta algo: alignment subsampling: 0.7 subsample_per_point: 1024 min_overlapping: 50 max_query_reads: 1000 use_portion_in_output: False sampling|min_sampling_portion: 0 sampling|max_sampling_portion: 1 sampling|sampling_portion_interval: 0.01 mating|use_rev_comp: False mating|n_as_mismatches: False mating|kmer_size: 24 seed: 1000 log_test: True json_object: True |
name: value name: value name: value name: value name: value |
test.fasta value |
| Test-2 |
input: test.fastq algo: kmer subsampling: 0.7 subsample_per_point: 1024 min_overlapping: 50 max_query_reads: 10 use_portion_in_output: False sampling|min_sampling_portion: 0 sampling|max_sampling_portion: 1 sampling|sampling_portion_interval: 0.01 mating|use_rev_comp: False mating|n_as_mismatches: False mating|kmer_size: 24 seed: 1000 log_test: False |
name: value name: value name: value |
test.fastq value |