| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/qfilt/qfilt/1.0.0+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/qfilt/qfilt/1.0.0 |
| qfilt |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| qfilt | 0.0.1 | package |
| Additional information about this tool |
qfilt -o '$filtered_output'
-f $output_format
#if str($options.advanced) == 'advanced':
-q $options.qscore
-l $options.length
$options.split
#if $options.replace and $options.remove:
-P '$options.replace'
-R '$options.remove'
#elif $options.mode:
-m $options.mode
#end if
#if $options.prefix:
-t $options.mismatch
-T '$options.prefix'
#end if
$options.tolerate_homopolymeric $options.tolerate_ambiguous
#end if
#if $input_data.format == 'fastq':
-Q
#if $input_data.fastq.ext.endswith('.gz')
<(zcat '$input_data.fastq')
#else
'$input_data.fastq'
#end if
#else:
-F '$input_data.fasta'
'$input_data.qual'
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_data|fastq: qfilt-in1.fastq |
name: value |
qfilt-in1.fastq value |
| Test-2 |
input_data|fastq: qfilt-in1.fastq.gz input_data|format: fastq options|tolerate_homopolymeric: False options|advanced: advanced |
name: value |
qfilt-in1.fastq.gz value |
| Test-3 |
input_data|fasta: qfilt-in2.fa input_data|qual: qfilt-in2.qual input_data|format: fastaq output_format: FASTQ |
name: value |
qfilt-in2.fa qfilt-in2.qual value |