Permalink
Cannot retrieve contributors at this time
Fetching contributors…
Cannot retrieve contributors at this time
| <tool id="sickle" name="Sickle" version="1.33"> | |
| <description>Windowed Adaptive Trimming of FastQ data</description> | |
| <command> | |
| sickle | |
| #if str($readtype.single_or_paired) == "se": | |
| se -f $input_single -o $output_single | |
| #if $input_single.ext == "fastq": | |
| -t sanger | |
| #else if $input_single.ext == "fastqsanger": | |
| -t sanger | |
| #else if $input_single.ext == "fastqillumina": | |
| -t illumina | |
| #else if $input_single.ext == "fastqsolexa": | |
| -t solexa | |
| #end if | |
| #end if | |
| #if str($readtype.single_or_paired) == "pe_combo": | |
| #if $readtype.output_n: | |
| pe -c $input_combo -M $output_combo | |
| #else | |
| pe -c $input_combo -m $output_combo -s $output_combo_single | |
| #end if | |
| #if $input_combo.ext == "fastq": | |
| -t sanger | |
| #else if $input_combo.ext == "fastqsanger": | |
| -t sanger | |
| #else if $input_combo.ext == "fastqillumina": | |
| -t illumina | |
| #else if $input_combo.ext == "fastqsolexa": | |
| -t solexa | |
| #end if | |
| #end if | |
| #if str($readtype.single_or_paired) == "pe_sep": | |
| pe -f $input_paired1 -r $input_paired2 -o $output_paired1 -p $output_paired2 -s $output_paired_single | |
| #if $input_paired1.ext == "fastq": | |
| -t sanger | |
| #else if $input_paired1.ext == "fastqsanger": | |
| -t sanger | |
| #else if $input_paired1.ext == "fastqillumina": | |
| -t illumina | |
| #else if $input_paired1.ext == "fastqsolexa": | |
| -t solexa | |
| #end if | |
| #end if | |
| #if str($qual_threshold) != "": | |
| -q $qual_threshold | |
| #end if | |
| #if str($length_threshold) != "": | |
| -l $length_threshold | |
| #end if | |
| #if $no_five_prime: | |
| -x | |
| #end if | |
| #if $trunc_n: | |
| -n | |
| #end if | |
| --quiet | |
| </command> | |
| <inputs> | |
| <conditional name="readtype"> | |
| <param name="single_or_paired" type="select" optional="false" label="Single-End or Paired-End reads?" help="Note: Sickle will infer the quality type of the file from its datatype. I.e., if the datatype is fastqsanger, then the quality type is sanger. The default is fastqsanger."> | |
| <option value="se" selected="true">Single-End</option> | |
| <option value="pe_combo">Paired-End (one interleaved input file)</option> | |
| <option value="pe_sep">Paired-End (two separate input files)</option> | |
| </param> | |
| <when value="se"> | |
| <param format="fastq, fastqsanger, fastqillumina, fastqsolexa" name="input_single" type="data" optional="false" label="Single-End FastQ Reads"/> | |
| </when> | |
| <when value="pe_combo"> | |
| <param format="fastq, fastqsanger, fastqillumina, fastqsolexa" name="input_combo" type="data" optional="false" label="Paired-End Interleaved FastQ Reads"/> | |
| <param name="output_n" type="boolean" label="Output only one file with all reads" help="This will output only one file with all the reads, where the reads that did not pass filter will be replaced with a single 'N', rather than discarded."/> | |
| </when> | |
| <when value="pe_sep"> | |
| <param format="fastq, fastqsanger, fastqillumina, fastqsolexa" name="input_paired1" type="data" optional="false" label="Paired-End Forward Strand FastQ Reads"/> | |
| <param format="fastq, fastqsanger, fastqillumina, fastqsolexa" name="input_paired2" type="data" optional="false" label="Paired-End Reverse Strand FastQ Reads"/> | |
| </when> | |
| </conditional> | |
| <param name="qual_threshold" value="20" type="integer" optional="true" label="Quality Threshold"> | |
| <validator type="in_range" min="0" message="Minimum value is 0"/> | |
| </param> | |
| <param name="length_threshold" value="20" type="integer" optional="true" label="Length Threshold"> | |
| <validator type="in_range" min="0" message="Minimum value is 0"/> | |
| </param> | |
| <param name="no_five_prime" type="boolean" label="Don't do 5' trimming"/> | |
| <param name="trunc_n" type="boolean" label="Truncate sequences with Ns at first N position"/> | |
| </inputs> | |
| <outputs> | |
| <data format_source="input_single" name="output_single" label="Single-End output of ${tool.name} on ${on_string}"> | |
| <filter>(readtype['single_or_paired'] == 'se')</filter> | |
| </data> | |
| <data format_source="input_combo" name="output_combo" label="Paired-End interleaved output of ${tool.name} on ${on_string}"> | |
| <filter>(readtype['single_or_paired'] == 'pe_combo')</filter> | |
| </data> | |
| <data format_source="input_combo" name="output_combo_single" label="Singletons from Paired-End interleaved output of ${tool.name} on ${on_string}"> | |
| <filter>(readtype['single_or_paired'] == 'pe_combo')</filter> | |
| <filter>(readtype['output_n'] == False)</filter> | |
| </data> | |
| <data format_source="input_paired1" name="output_paired1" label="Paired-End forward strand output of ${tool.name} on ${on_string}"> | |
| <filter>(readtype['single_or_paired'] == 'pe_sep')</filter> | |
| </data> | |
| <data format_source="input_paired2" name="output_paired2" label="Paired-End reverse strand output of ${tool.name} on ${on_string}"> | |
| <filter>(readtype['single_or_paired'] == 'pe_sep')</filter> | |
| </data> | |
| <data format_source="input_paired1" name="output_paired_single" label="Singletons from Paired-End output of ${tool.name} on ${on_string}"> | |
| <filter>(readtype['single_or_paired'] == 'pe_sep')</filter> | |
| </data> | |
| </outputs> | |
| <help> | |
| **Sickle - A windowed adaptive trimming tool for FASTQ files using quality** | |
| .. class:: infomark | |
| **About** | |
| Most modern sequencing technologies produce reads that have | |
| deteriorating quality towards the 3'-end and some towards the 5'-end | |
| as well. Incorrectly called bases in both regions negatively impact | |
| assembles, mapping, and downstream bioinformatics analyses. | |
| Sickle is a tool that uses sliding windows along with quality and | |
| length thresholds to determine when quality is sufficiently low to | |
| trim the 3'-end of reads and also determines when the quality is | |
| sufficiently high enough to trim the 5'-end of reads. It will also | |
| discard reads based upon the length threshold. It takes the quality | |
| values and slides a window across them whose length is 0.1 times the | |
| length of the read. If this length is less than 1, then the window is | |
| set to be equal to the length of the read. Otherwise, the window | |
| slides along the quality values until the average quality in the | |
| window rises above the threshold, at which point the algorithm | |
| determines where within the window the rise occurs and cuts the read | |
| and quality there for the 5'-end cut. Then when the average quality | |
| in the window drops below the threshold, the algorithm determines | |
| where in the window the drop occurs and cuts both the read and quality | |
| strings there for the 3'-end cut. However, if the length of the | |
| remaining sequence is less than the minimum length threshold, then the | |
| read is discarded entirely (or replaced with an "N" record). 5'-end | |
| trimming can be disabled. Sickle also has an option to truncate reads | |
| with Ns at the first N position. | |
| Sickle supports three types of quality values: Illumina, Solexa, and | |
| Sanger. Note that the Solexa quality setting is an approximation (the | |
| actual conversion is a non-linear transformation). The end | |
| approximation is close. Illumina quality refers to qualities encoded | |
| with the CASAVA pipeline between versions 1.3 and 1.7. Illumina | |
| quality using CASAVA >= 1.8 is Sanger encoded. The quality value will | |
| be determined from the datatype of the data, i.e. a fastqsanger datatype | |
| is assumed to be Sanger encoded. | |
| Note that Sickle will remove the 2nd fastq record header (on the "+" | |
| line) and replace it with simply a "+". This is the default format for | |
| CASAVA >= 1.8. | |
| ----- | |
| .. class:: infomark | |
| **Options** | |
| **Single-end** | |
| This option takes one single-end input file and outputs one single-end | |
| output file of reads that passed the filters. | |
| **Paired-End (one interleaved input file)** | |
| This option takes as input one interleaved paired-end file. If you then | |
| check the "Output only one file with all reads" checkbox, it will output | |
| one interleaved file where any read that did not pass filter will be replaced | |
| with a FastQ record where the sequence is a single "N" and the quality is the | |
| lowest quality possible for that quality type. This will preserve the paired | |
| nature of the data. If you leave the checkbox unchecked, it will output two files, | |
| one interleaved file with all the passed pairs and one singletons file where only | |
| one of the pair passed filter. | |
| **Paired-End (two separate input files)** | |
| This option takes two separate (forward and reverse) paired-end files as input. | |
| The output is three files: Two paired-end files with pairs that passed filter and | |
| a singletons file where only one of the pair passed filter. | |
| **Quality threshold** | |
| Input your desired quality threshold. This threshold is phred-scaled, which is typically | |
| values between 0-41 for FastQ data. | |
| **Length threshold** | |
| Input your desired length threshold. This is the threshold to determine if a read is kept | |
| after all the trimming steps are done. | |
| **Disable 5-prime trimming** | |
| An option to disable trimming the read on the 5-prime end. This trimming trims the read | |
| if the average quality values dip below the quality threshold at the 5-prime end. | |
| **Truncate sequences with Ns** | |
| This option will trim a read at the first "N" base in the read after doing quality trimming. | |
| It is then still subject to the length threshold. | |
| ----- | |
| .. class:: infomark | |
| **Citation** | |
| Sickle doesn't have a paper, but you can cite it like this:: | |
| Joshi NA, Fass JN. (2011). Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files | |
| (Version 1.33) [Software]. Available at https://github.com/najoshi/sickle. | |
| ----- | |
| Copyright: Nikhil Joshi | |
| http://bioinformatics.ucdavis.edu | |
| http://github.com/ucdavis-bioinformatics | |
| http://github.com/najoshi | |
| </help> | |
| </tool> |