# HG changeset patch
# User slegras
# Date 1443383569 14400
# Node ID 1405432d1b9c0d2243ebe4ecfb2dabbc467411e6
Uploaded
diff -r 000000000000 -r 1405432d1b9c sickle.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/sickle.xml Sun Sep 27 15:52:49 2015 -0400
@@ -0,0 +1,254 @@
+
+ Windowed Adaptive Trimming of FastQ data
+
+ sickle
+
+
+ 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
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+ (readtype['single_or_paired'] == 'se')
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+ (readtype['single_or_paired'] == 'pe_combo')
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+ (readtype['single_or_paired'] == 'pe_combo')
+ (readtype['output_n'] == False)
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+ (readtype['single_or_paired'] == 'pe_sep')
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+ (readtype['single_or_paired'] == 'pe_sep')
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+ (readtype['single_or_paired'] == 'pe_sep')
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+
+**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
+
+
+
+
diff -r 000000000000 -r 1405432d1b9c tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Sun Sep 27 15:52:49 2015 -0400
@@ -0,0 +1,6 @@
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