# HG changeset patch
# User nikhil-joshi
# Date 1375845054 14400
# Node ID e52679b4470007a24e2dccf4778b1e54330711dd
# Parent 7b37c85ba925d9cc5049bc32baa1ff648032fd61
Uploaded
diff -r 7b37c85ba925 -r e52679b44700 sickle/sickle.xml
--- a/sickle/sickle.xml Tue Aug 06 23:10:08 2013 -0400
+++ b/sickle/sickle.xml Tue Aug 06 23:10:54 2013 -0400
@@ -5,11 +5,33 @@
sickle $readtype.single_or_paired --quiet
#if str($readtype.single_or_paired) == "se":
- -f $input_single -t $qual_type -o $output_single
+ -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":
- -f $input_paired1 -r $input_paired2 -o $output_paired1 -p $output_paired2 -s $output_paired_single -t $qual_type
+ -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_single.ext == "fastqsanger":
+ -t sanger
+ #else if $input_single.ext == "fastqillumina":
+ -t illumina
+ #else if $input_single.ext == "fastqsolexa":
+ -t solexa
+ #end if
+
#end if
#if str($qual_threshold) != "":
@@ -31,27 +53,21 @@
-
+
-
+
-
-
+
+
-
-
-
-
-
-
@@ -65,19 +81,19 @@
-
+
(readtype['single_or_paired'] == 'se')
-
+
(readtype['single_or_paired'] == 'pe')
-
+
(readtype['single_or_paired'] == 'pe')
-
+
(readtype['single_or_paired'] == 'pe')
@@ -89,11 +105,15 @@
Sickle also has an option to discard reads with any Ns in them.
-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.
+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. Sickle will get the quality type from the datatype of the file.
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.
Sickle also supports gzipped file inputs.
+
+Copyright: Nikhil Joshi
+http://bioinformatics.ucdavis.edu
+http://github.com/ucdavis-bioinformatics