| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/pear/iuc_pear/0.9.6.2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/pear/iuc_pear/0.9.6.1 |
| toolshed.g2.bx.psu.edu/repos/iuc/pear/iuc_pear/0.9.6.0 |
| iuc_pear |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| pear | 0.9.6 | package |
| Additional information about this tool |
pear
#if str( $library.type ) == "paired":
-f "$library.forward"
-r "$library.reverse"
#if $library.forward.is_of_type( 'fastqillumina' ):
--phred-base 64
#else:
--phred-base 33
#end if
#else
## prepare collection
-f "$library.input_collection.forward"
-r "$library.input_collection.reverse"
#if $library.input_collection.forward.is_of_type( 'fastqillumina' ):
--phred-base 64
#else:
--phred-base 33
#end if
#end if
--output pear
--p-value $pvalue
--min-overlap $min_overlap
#if int($max_assembly_length) > 0:
--max-asm-length $max_assembly_length
#end if
--min-asm-length $min_assembly_length
--min-trim-length $min_trim_length
--quality-theshold $quality_threshold
--max-uncalled-base $max_uncalled_base
--test-method $test_method
--empirical-freqs $empirical_freqs
-j "\${GALAXY_SLOTS:-8}"
--score-method $score_method
--cap $cap
$nbase
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
library|forward: forward.fastq library|reverse: reverse.fastq library|type: paired min_overlap: 10 min_assembly_length: 50 cap: 0 outputs: ['assembled', 'unassembled_forward'] |
name: value name: value |
forward.fastq reverse.fastq value |
| Test-2 |
library|input_collection: paired collection library|type: paired_collection min_overlap: 10 min_assembly_length: 50 cap: 0 outputs: ['assembled', 'unassembled_forward'] |
name: value name: value |
forward.fastq reverse.fastq value |