--- a/scythe/LICENSE	Tue Aug 06 23:17:08 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-MIT License
-Permission is hereby granted, free of charge, to any person
-obtaining a copy of this software and associated documentation
-files (the "Software"), to deal in the Software without
-restriction, including without limitation the rights to use, copy,
-modify, merge, publish, distribute, sublicense, and/or sell copies
-of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
-BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
-ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
-CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.

--- a/scythe/README.md	Tue Aug 06 23:17:08 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,191 +0,0 @@
-# Scythe - A very simple adapter trimmer (version 0.981 BETA)
-
-Scythe and all supporting documentation 
-Copyright (c) Vince Buffalo, 2011-2012
-
-Contact: Vince Buffalo <vsbuffaloAAAAA@gmail.com> (with the poly-A tail removed)
-
-If you wish to report a bug, please open an issue on Github
-(http://github.com/vsbuffalo/scythe/issues) so that it can be
-tracked. You can contact me as well, but please open an issue first.
-
-## About
-
-Scythe uses a Naive Bayesian approach to classify contaminant
-substrings in sequence reads. It considers quality information, which
-can make it robust in picking out 3'-end adapters, which often include
-poor quality bases.
-
-Most next generation sequencing reads have deteriorating quality
-towards the 3'-end. It's common for a quality-based trimmer to be
-employed before mapping, assemblies, and analysis to remove these poor
-quality bases. However, quality-based trimming could remove bases that
-are helpful in identifying (and removing) 3'-end adapter
-contaminants. Thus, it is recommended you run Scythe *before*
-quality-based trimming, as part of a read quality control pipeline.
-
-The Bayesian approach Scythe uses compares two likelihood models: the
-probability of seeing the matches in a sequence given contamination,
-and not given contamination. Given that the read is contaminated, the
-probability of seeing a certain number of matches and mistmatches is a
-function of the quality of the sequence. Given the read is not
-contaminated (and is thus assumed to be random sequence), the
-probability of seeing a certain number of matches and mismatches is
-chance. The posterior is calculated across both these likelihood
-models, and the class (contaminated or not contaminated) with the
-maximum posterior probability is the class selected.
-
-## Requirements
-
-Scythe can be compiled using GCC or Clang; compilation during
-development used the latter. Scythe relies on Heng Li's kseq.h, which
-is bundled with the source.
-
-Scythe requires Zlib, which can be obtained at <http://www.zlib.net/>.
-
-## Building and Installing Scythe
-
-To build Scythe, enter:
-
-    make build
-
-Then, copy or move "scythe" to a directory in your $PATH.
-
-## Usage
-
-Scythe can be run minimally with:
-
-    scythe -a adapter_file.fasta -o trimmed_sequences.fasta sequences.fastq
-
-By default, the prior contamination rate is 0.05. This can be changed
-(and one is encouraged to do so!) with:
-
-    scythe -a adapter_file.fasta -p 0.1 -o trimmed_sequences.fastq sequences.fastq
-
-If you'd like to use standard out, it is recommended you use the
---quiet option:
-
-    scythe -a adapter_file.fasta --quiet sequences.fastq > trimmed_sequences.fastq
-
-Also, more detailed output about matches can be obtained with:
-
-    scythe -a adapter_file.fasta -o trimmed_sequences.fasta -m matches.txt sequences.fastq
-
-By default, Illumina's quality scheme (pipeline > 1.3) is used. Sanger
-or Solexa (pipeline < 1.3) qualities can be specified with -q:
-
-    scythe -a adapter_file.fasta -q solexa -o trimmed_sequences.fasta sequences.fastq
-
-Lastly, a minimum match length argument can be specified with -n <integer>:
-
-    scythe -a adapter_file.fasta -n 0 -o trimmed_sequences.fasta sequences.fastq
-
-The default is 5. If this pre-processing is upstream of assembly on a
-very contaminated lane, decreasing this parameter could lead to *very*
-liberal trimming, i.e. of only a few bases. 
-
-## Notes
-
-Scythe only checks for 3'-end contaminants, up to the adapter's length
-into the 3'-end. For reads with contamination in *any* position, the
-program TagDust (<http://genome.gsc.riken.jp/osc/english/dataresource/>)
-is recommended. Scythe has the advantages of allowing fuzzier matching
-and being base quality-aware, while TagDust has the advantages of very
-fast matching (but allowing few mismatches, and not considering
-quality) and FDR. TagDust also removes contaminated reads *entirely*, while
-Scythe trims off contaminants. 
-
-A possible pipeline would run FASTQ reads through Scythe, then
-TagDust, then a quality-based trimmer, and finally through a read
-quality statistics program such as qrqc
-(<http://bioconductor.org/packages/devel/bioc/html/qrqc.html>) or FASTqc
-(<http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/>).
-
-## FAQ 
-
-### Does Scythe work with paired-end data?
-
-Scythe does work with paired-end data. Each file must be run
-separately, but Scythe will not remove reads entirely leaving
-mismatched pairs.
-
-In some cases, barcodes are ligated to both the 3'-end and 5'-end of
-reads. 5'-end removal is trivial since base calling is near-perfect
-there, but 3'-end removal can be trickier. Some users have created
-Scythe adapter files that contain all possible barcodes concatenated
-with possible adapters, so that both can be recognized and
-removed. This has worked well and is recommended for cases when 3'-end
-quality deteriorates and prevents barcode removal. Newer Illumina
-chemistry has the barcode separated from the fragment, so that it
-appears as an entirely separate read and is used to demultiplex sample
-reads by Illumina's CASAVA pipeline.
-
-### Does Scythe work on 5'-end or other contaminants?
-
-No. Embracing the Unix tool philosophy that tools should do one thing
-very well, Scythe just removes 3'-end contaminants where there could
-be multiple base mismatches due to poor base quality. N-mismatch
-algorithms (such as TagDust) don't consider base qualities. Scythe
-will allow more mismatches in an alignment if the mismatched bases are
-of low quality.
-
-**Scythe only checks as far in as the entire adapter contaminant's
-length.** However, some investigation has shown that Illumina
-pipelines sometimes produce reads longer than the read length +
-adapter length. The extra bases have always been observed to be
-A's. Some testing has shown this can be addressed by appending A's to
-the adapters in the adapters file. Since Scythe begins by checking for
-contamination from the 5'-end of the adapter, this won't affect the
-normal adapter contaminant cases.
-
-### What does the numeric output from Scythe mean?
-
-For each adapter in the file, the contaminants removed by position are
-returned via standard error. For example:
-
-    Adapter 1 'fake adapter' contamination occurences:
-    [10, 2, 4, 5, 6]
-
-indicates that "fake adapter" is 5 bases long (the length of the array
-returned), and that there were 10 contaminants found of first base (-n
-was set to 0 then), 2 of the first two bases, 4 contaminants of the
-first 3 bases, 5 of the first 4 bases, etc.
-
-### Does Scythe work on FASTA files?
-
-No, as these have no quality information.
-
-### How can I report a bug? 
-
-See the section below.
-
-### How does Scythe compare to program "x"?
-
-As far as I know, Scythe is the only program that employs a Bayesian
-model that allows prior contaminant estimates to be used. This prior
-is a more realistic approach than setting a fixed number of mismatches
-because we can visually estimate it with the Unix tool `less`.
-
-Scythe also looks at base-level qualities, *not* just a fixed level of
-mismatches. A fixed number of mismatches is a bad approach with data
-our group (the UC Davis Bioinformatics Core) has seen, as a small bad
-quality run can quickly exhaust even a high numbers of fixed
-mismatches and lead to higher false negatives.
-
-## Reporting Bugs
-
-Scythe is free software and is proved without a warranty. However, I
-am proud of this software and I will do my best to provide updates,
-bug fixes, and additional documentation as needed. Please report all
-bugs and issues to Github's issue tracker
-(http://github.com/vsbuffalo/scythe/issues). If you want to email me,
-do so in addition to an issue request.
-
-If you have a suggestion or comment on Scythe's methods, you can email
-me directly.
-
-## Is there a paper about Scythe?
-
-I am currently writing a paper on Scythe's methods. In my preliminary
-testing, Scythe has fewew false positives and false negatives than
-it competitors.
\ No newline at end of file

--- a/scythe/illumina_adapters.fa	Tue Aug 06 23:17:08 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
->Multiplexing_adapter_1
-GATCGGAAGAGCACACGTCT
->Multiplexing_adapter_2
-CACTCTTTCCCTACACGACGCTCTTCCGATCT

Binary file scythe/scythe has changed

--- a/scythe/scythe.xml	Tue Aug 06 23:17:08 2013 -0400
+++ b/scythe/scythe.xml	Tue Mar 10 20:37:06 2015 -0400
@@ -1,8 +1,8 @@
-<tool id="scythe" name="Scythe">
+<tool id="scythe" name="Scythe" version="0.991">
 	<description>Trimming adapters/contaminants using a Naive Bayesian classifier</description>
 
 	<command>
-		scythe --quiet -a $adapter_file
+		scythe -a $adapter_file
 
                 #if $input_fastq.ext == "fastq":
                 -q sanger
@@ -34,7 +34,7 @@
 		-m $output_matches
 		#end if
 
-		-o $output_trimmed $input_fastq 2> /dev/null
+		-o $output_trimmed $input_fastq 2>&amp;1
 	</command>
 
 	<inputs>

--- a/scythe/truseq_adapters.fasta	Tue Aug 06 23:17:08 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
->TruSeq_forward_contam
-AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC[NNNNNN]ATCTCGTATGCCGTCTTCTGCTTGAAAAA
->TruSeq_reverse_contam
-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAA