# HG changeset patch
# User peterjc
# Date 1382621845 14400
# Node ID ee5acea162a7744cd8f452fa298466cf67a95ac4
# Parent  8c02a91a868019bbb9e57ea03a05a6f5b86d4df6
Uploaded v0.0.10, README now using RST, MIT licence, automatic Biopython dependency

diff -r 8c02a91a8680 -r ee5acea162a7 tools/primers/seq_primer_clip.py
--- a/tools/primers/seq_primer_clip.py	Tue Apr 30 11:04:43 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,358 +0,0 @@
-#!/usr/bin/env python
-"""Looks for the given primer sequences and clips matching SFF reads.
-
-Takes eight command line options, input read filename, input read format,
-input primer FASTA filename, type of primers (forward, reverse or reverse-
-complement), number of mismatches (currently only 0, 1 and 2 are supported),
-minimum length to keep a read (after primer trimming), should primer-less
-reads be kept (boolean), and finally the output sequence filename.
-
-Both the primer and read sequences can contain IUPAC ambiguity codes like N.
-
-This supports FASTA, FASTQ and SFF sequence files. Colorspace reads are not
-supported.
-
-The mismatch parameter does not consider gapped alignemnts, however the
-special case of missing bases at the very start or end of the read is handled.
-e.g. a primer sequence CCGACTCGAG will match a read starting CGACTCGAG...
-if one or more mismatches are allowed.
-
-This can also be used for stripping off (and optionally filtering on) barcodes.
-
-Note that only the trim/clip values in the SFF file are changed, not the flow
-information of the full read sequence.
-
-This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute
-(formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved.
-See accompanying text file for licence details (MIT/BSD style).
-
-This is version 0.0.8 of the script. Currently it uses Python's regular
-expression engine for finding the primers, which for my needs is fast enough.
-"""
-import sys
-import re
-from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
-from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
-
-if "-v" in sys.argv or "--version" in sys.argv:
-    print "v0.0.5"
-    sys.exit(0)
-
-def stop_err(msg, err=1):
-    sys.stderr.write(msg)
-    sys.exit(err)
-
-try:
-    from Bio.Seq import reverse_complement
-    from Bio.SeqIO.SffIO import SffIterator, SffWriter
-except ImportError:
-    stop_err("Requires Biopython 1.54 or later")
-try:
-    from Bio.SeqIO.SffIO import ReadRocheXmlManifest
-except ImportError:
-    #Prior to Biopython 1.56 this was a private function
-    from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest
-
-#Parse Command Line
-try:
-    in_file, seq_format, primer_fasta, primer_type, mm, min_len, keep_negatives, out_file = sys.argv[1:]
-except ValueError:
-    stop_err("Expected 8 arguments, got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv)))
-
-if in_file == primer_fasta:
-    stop_err("Same file given as both primer sequences and sequences to clip!")
-if in_file == out_file:
-    stop_err("Same file given as both sequences to clip and output!")
-if primer_fasta == out_file:
-    stop_err("Same file given as both primer sequences and output!")
-
-try:
-    mm = int(mm)
-except ValueError:
-    stop_err("Expected non-negative integer number of mismatches (e.g. 0 or 1), not %r" % mm)
-if mm < 0:
-    stop_err("Expected non-negtive integer number of mismatches (e.g. 0 or 1), not %r" % mm)
-if mm not in [0,1,2]:
-    raise NotImplementedError
-
-try:
-    min_len = int(min_len)
-except ValueError:
-    stop_err("Expected non-negative integer min_len (e.g. 0 or 1), not %r" % min_len)
-if min_len < 0:
-    stop_err("Expected non-negtive integer min_len (e.g. 0 or 1), not %r" % min_len)
-
-
-if keep_negatives.lower() in ["true", "yes", "on"]:
-    keep_negatives = True
-elif keep_negatives.lower() in ["false", "no", "off"]:
-    keep_negatives = False
-else:
-    stop_err("Expected boolean for keep_negatives (e.g. true or false), not %r" % keep_negatives)
-
-
-if primer_type.lower() == "forward":
-    forward = True
-    rc = False
-elif primer_type.lower() == "reverse":
-    forward = False
-    rc = False
-elif primer_type.lower() == "reverse-complement":
-    forward = False
-    rc = True
-else:
-    stop_err("Expected foward, reverse or reverse-complement not %r" % primer_type)
-
-
-ambiguous_dna_values = {
-    "A": "A",
-    "C": "C",
-    "G": "G",
-    "T": "T",
-    "M": "ACM",
-    "R": "AGR",
-    "W": "ATW",
-    "S": "CGS",
-    "Y": "CTY",
-    "K": "GTK",
-    "V": "ACGMRSV",
-    "H": "ACTMWYH",
-    "D": "AGTRWKD",
-    "B": "CGTSYKB",
-    "X": ".", #faster than [GATCMRWSYKVVHDBXN] or even [GATC]
-    "N": ".",
-    }
-
-ambiguous_dna_re = {}
-for letter, values in ambiguous_dna_values.iteritems():
-    if len(values) == 1:
-        ambiguous_dna_re[letter] = values
-    else:
-        ambiguous_dna_re[letter] = "[%s]" % values
-
-
-def make_reg_ex(seq):
-    return "".join(ambiguous_dna_re[letter] for letter in seq)
-
-def make_reg_ex_mm(seq, mm):
-    if mm > 2:
-        raise NotImplementedError("At most 2 mismatches allowed!")
-    seq = seq.upper()
-    yield make_reg_ex(seq)
-    for i in range(1,mm+1):
-        #Missing first/last i bases at very start/end of sequence
-        for reg in make_reg_ex_mm(seq[i:],  mm-i):
-            yield "^" + reg
-        for reg in make_reg_ex_mm(seq[:-i], mm-i):
-            yield "$" + reg
-    if mm >= 1:
-        for i,letter in enumerate(seq):
-            #We'll use a set to remove any duplicate patterns
-            #if letter not in "NX":
-            pattern = seq[:i] + "N" + seq[i+1:]
-            assert len(pattern) == len(seq), "Len %s is %i, len %s is %i" \
-                   % (pattern, len(pattern), seq, len(seq))
-            yield make_reg_ex(pattern)
-    if mm >=2:
-        for i,letter in enumerate(seq):
-            #We'll use a set to remove any duplicate patterns
-            #if letter not in "NX":
-            for k,letter in enumerate(seq[i+1:]):
-                #We'll use a set to remove any duplicate patterns
-                #if letter not in "NX":
-                pattern = seq[:i] + "N" + seq[i+1:i+1+k] + "N" + seq[i+k+2:]
-                assert len(pattern) == len(seq), "Len %s is %i, len %s is %i" \
-                       % (pattern, len(pattern), seq, len(seq))
-                yield make_reg_ex(pattern)
-
-def load_primers_as_re(primer_fasta, mm, rc=False):
-    #Read primer file and record all specified sequences
-    primers = set()
-    in_handle = open(primer_fasta, "rU")
-    reader = fastaReader(in_handle)
-    count = 0
-    for record in reader:
-        if rc:
-            seq = reverse_complement(record.sequence)
-        else:
-            seq = record.sequence
-        #primers.add(re.compile(make_reg_ex(seq)))
-        count += 1
-        for pattern in make_reg_ex_mm(seq, mm):
-            primers.add(pattern)
-    in_handle.close()
-    #Use set to avoid duplicates, sort to have longest first
-    #(so more specific primers found before less specific ones)
-    primers = sorted(set(primers), key=lambda p: -len(p))
-    return count, re.compile("|".join(primers)) #make one monster re!
-
-
-
-#Read primer file and record all specified sequences
-count, primer = load_primers_as_re(primer_fasta, mm, rc)
-print "%i primer sequences" % count
-
-short_neg = 0
-short_clipped = 0
-clipped = 0
-negs = 0
-
-if seq_format.lower()=="sff":
-    #SFF is different because we just change the trim points
-    if forward:
-        def process(records):
-            global short_clipped, short_neg, clipped, negs
-            for record in records:
-                left_clip = record.annotations["clip_qual_left"]
-                right_clip = record.annotations["clip_qual_right"]
-                seq = str(record.seq)[left_clip:right_clip].upper()
-                result = primer.search(seq)
-                if result:
-                    #Forward primer, take everything after it
-                    #so move the left clip along
-                    if len(seq) - result.end() >= min_len:
-                        record.annotations["clip_qual_left"] = left_clip + result.end()
-                        clipped += 1
-                        yield record
-                    else:
-                        short_clipped += 1
-                elif keep_negatives:
-                    if len(seq) >= min_len:
-                        negs += 1
-                        yield record
-                    else:
-                        short_neg += 1
-    else:
-        def process(records):
-            global short_clipped, short_neg, clipped, negs
-            for record in records:
-                left_clip = record.annotations["clip_qual_left"]
-                right_clip = record.annotations["clip_qual_right"]
-                seq = str(record.seq)[left_clip:right_clip].upper()
-                result = primer.search(seq)
-                if result:
-                    #Reverse primer, take everything before it
-                    #so move the right clip back
-                    new_len = result.start()
-                    if new_len >= min_len:
-                        record.annotations["clip_qual_right"] = left_clip + new_len
-                        clipped += 1
-                        yield record
-                    else:
-                        short_clipped += 1
-                elif keep_negatives:
-                    if len(seq) >= min_len:
-                        negs += 1
-                        yield record
-                    else:
-                        short_neg += 1
-    
-    in_handle = open(in_file, "rb")
-    try:
-        manifest = ReadRocheXmlManifest(in_handle)
-    except ValueError:
-        manifest = None
-    in_handle.seek(0)
-    out_handle = open(out_file, "wb")
-    writer = SffWriter(out_handle, xml=manifest)
-    writer.write_file(process(SffIterator(in_handle)))
-    #End of SFF code
-elif seq_format.lower().startswith("fastq"):
-    in_handle = open(in_file, "rU")
-    out_handle = open(out_file, "w")
-    reader = fastqReader(in_handle)
-    writer = fastqWriter(out_handle)
-    if forward:
-        for record in reader:
-            seq = record.sequence.upper()
-            result = primer.search(seq)
-            if result:
-                #Forward primer, take everything after it
-                cut = result.end()
-                record.sequence = seq[cut:]
-                if len(record.sequence) >= min_len:
-                    record.quality = record.quality[cut:]
-                    clipped += 1
-                    writer.write(record)
-                else:
-                    short_clipped += 1
-            elif keep_negatives:
-                if len(record) >= min_len:
-                    negs += 1
-                    writer.write(record)
-                else:
-                    short_negs += 1
-    else:
-        for record in reader:
-            seq = record.sequence.upper()
-            result = primer.search(seq)
-            if result:
-                #Reverse primer, take everything before it
-                cut = result.start()
-                record.sequence = seq[:cut]
-                if len(record.sequence) >= min_len:
-                    record.quality = record.quality[:cut]
-                    clipped += 1
-                    writer.write(record)
-                else:
-                    short_clipped += 1
-            elif keep_negatives:
-                if len(record) >= min_len:
-                    negs += 1
-                    writer.write(record)
-                else:
-                    short_negs += 1
-elif seq_format.lower()=="fasta":
-    in_handle = open(in_file, "rU")
-    out_handle = open(out_file, "w")
-    reader = fastaReader(in_handle)
-    writer = fastaWriter(out_handle)
-    #Following code is identical to that for FASTQ but without editing qualities
-    if forward:
-        for record in reader:
-            seq = record.sequence.upper()
-            result = primer.search(seq)
-            if result:
-                #Forward primer, take everything after it
-                cut = result.end()
-                record.sequence = seq[cut:]
-                if len(record.sequence) >= min_len:
-                    clipped += 1
-                    writer.write(record)
-                else:
-                    short_clipped += 1
-            elif keep_negatives:
-                if len(record) >= min_len:
-                    negs += 1
-                    writer.write(record)
-                else:
-                    short_negs += 1
-    else:
-        for record in reader:
-            seq = record.sequence.upper()
-            result = primer.search(seq)
-            if result:
-                #Reverse primer, take everything before it
-                cut = result.start()
-                record.sequence = seq[:cut]
-                if len(record.sequence) >= min_len:
-                    clipped += 1
-                    writer.write(record)
-                else:
-                    short_clipped += 1
-            elif keep_negatives:
-                if len(record) >= min_len:
-                    negs += 1
-                    writer.write(record)
-                else:
-                    short_negs += 1
-else:
-    stop_err("Unsupported file type %r" % seq_format)
-in_handle.close()
-out_handle.close()
-
-print "Kept %i clipped reads," % clipped
-print "discarded %i short." % short_clipped
-if keep_negatives:
-    print "Kept %i non-matching reads," % negs
-    print "discarded %i short." % short_neg
diff -r 8c02a91a8680 -r ee5acea162a7 tools/primers/seq_primer_clip.py.orig
--- a/tools/primers/seq_primer_clip.py.orig	Tue Apr 30 11:04:43 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,358 +0,0 @@
-#!/usr/bin/env python
-"""Looks for the given primer sequences and clips matching SFF reads.
-
-Takes eight command line options, input read filename, input read format,
-input primer FASTA filename, type of primers (forward, reverse or reverse-
-complement), number of mismatches (currently only 0, 1 and 2 are supported),
-minimum length to keep a read (after primer trimming), should primer-less
-reads be kept (boolean), and finally the output sequence filename.
-
-Both the primer and read sequences can contain IUPAC ambiguity codes like N.
-
-This supports FASTA, FASTQ and SFF sequence files. Colorspace reads are not
-supported.
-
-The mismatch parameter does not consider gapped alignemnts, however the
-special case of missing bases at the very start or end of the read is handled.
-e.g. a primer sequence CCGACTCGAG will match a read starting CGACTCGAG...
-if one or more mismatches are allowed.
-
-This can also be used for stripping off (and optionally filtering on) barcodes.
-
-Note that only the trim/clip values in the SFF file are changed, not the flow
-information of the full read sequence.
-
-This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute
-(formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved.
-See accompanying text file for licence details (MIT/BSD style).
-
-This is version 0.0.8 of the script. Currently it uses Python's regular
-expression engine for finding the primers, which for my needs is fast enough.
-"""
-import sys
-import re
-from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
-from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
-
-if "-v" in sys.argv or "--version" in sys.argv:
-    print "v0.0.5"
-    sys.exit(0)
-
-def stop_err(msg, err=1):
-    sys.stderr.write(msg)
-    sys.exit(err)
-
-try:
-    from Bio.Seq import reverse_complement
-    from Bio.SeqIO.SffIO import SffIterator, SffWriter
-except ImportError:
-    stop_err("Requires Biopython 1.54 or later")
-try:
-    from Bio.SeqIO.SffIO import ReadRocheXmlManifest
-except ImportError:
-    #Prior to Biopython 1.56 this was a private function
-    from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest
-
-#Parse Command Line
-try:
-    in_file, seq_format, primer_fasta, primer_type, mm, min_len, keep_negatives, out_file = sys.argv[1:]
-except ValueError:
-    stop_err("Expected 8 arguments, got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv)))
-
-if in_file == primer_fasta:
-    stop_err("Same file given as both primer sequences and sequences to clip!")
-if in_file == out_file:
-    stop_err("Same file given as both sequences to clip and output!")
-if primer_fasta == out_file:
-    stop_err("Same file given as both primer sequences and output!")
-
-try:
-    mm = int(mm)
-except ValueError:
-    stop_err("Expected non-negative integer number of mismatches (e.g. 0 or 1), not %r" % mm)
-if mm < 0:
-    stop_err("Expected non-negtive integer number of mismatches (e.g. 0 or 1), not %r" % mm)
-if mm not in [0,1,2]:
-    raise NotImplementedError
-
-try:
-    min_len = int(min_len)
-except ValueError:
-    stop_err("Expected non-negative integer min_len (e.g. 0 or 1), not %r" % min_len)
-if min_len < 0:
-    stop_err("Expected non-negtive integer min_len (e.g. 0 or 1), not %r" % min_len)
-
-
-if keep_negatives.lower() in ["true", "yes", "on"]:
-    keep_negatives = True
-elif keep_negatives.lower() in ["false", "no", "off"]:
-    keep_negatives = False
-else:
-    stop_err("Expected boolean for keep_negatives (e.g. true or false), not %r" % keep_negatives)
-
-
-if primer_type.lower() == "forward":
-    forward = True
-    rc = False
-elif primer_type.lower() == "reverse":
-    forward = False
-    rc = False
-elif primer_type.lower() == "reverse-complement":
-    forward = False
-    rc = True
-else:
-    stop_err("Expected foward, reverse or reverse-complement not %r" % primer_type)
-
-
-ambiguous_dna_values = {
-    "A": "A",
-    "C": "C",
-    "G": "G",
-    "T": "T",
-    "M": "ACM",
-    "R": "AGR",
-    "W": "ATW",
-    "S": "CGS",
-    "Y": "CTY",
-    "K": "GTK",
-    "V": "ACGMRSV",
-    "H": "ACTMWYH",
-    "D": "AGTRWKD",
-    "B": "CGTSYKB",
-    "X": ".", #faster than [GATCMRWSYKVVHDBXN] or even [GATC]
-    "N": ".",
-    }
-
-ambiguous_dna_re = {}
-for letter, values in ambiguous_dna_values.iteritems():
-    if len(values) == 1:
-        ambiguous_dna_re[letter] = values
-    else:
-        ambiguous_dna_re[letter] = "[%s]" % values
-
-
-def make_reg_ex(seq):
-    return "".join(ambiguous_dna_re[letter] for letter in seq)
-
-def make_reg_ex_mm(seq, mm):
-    if mm > 2:
-        raise NotImplementedError("At most 2 mismatches allowed!")
-    seq = seq.upper()
-    yield make_reg_ex(seq)
-    for i in range(1,mm+1):
-        #Missing first/last i bases at very start/end of sequence
-        for reg in make_reg_ex_mm(seq[i:],  mm-i):
-            yield "^" + reg
-        for reg in make_reg_ex_mm(seq[:-i], mm-i):
-            yield "$" + reg
-    if mm >= 1:
-        for i,letter in enumerate(seq):
-            #We'll use a set to remove any duplicate patterns
-            #if letter not in "NX":
-            pattern = seq[:i] + "N" + seq[i+1:]
-            assert len(pattern) == len(seq), "Len %s is %i, len %s is %i" \
-                   % (pattern, len(pattern), seq, len(seq))
-            yield make_reg_ex(pattern)
-    if mm >=2:
-        for i,letter in enumerate(seq):
-            #We'll use a set to remove any duplicate patterns
-            #if letter not in "NX":
-            for k,letter in enumerate(seq[i+1:]):
-                #We'll use a set to remove any duplicate patterns
-                #if letter not in "NX":
-                pattern = seq[:i] + "N" + seq[i+1:i+1+k] + "N" + seq[i+k+2:]
-                assert len(pattern) == len(seq), "Len %s is %i, len %s is %i" \
-                       % (pattern, len(pattern), seq, len(seq))
-                yield make_reg_ex(pattern)
-
-def load_primers_as_re(primer_fasta, mm, rc=False):
-    #Read primer file and record all specified sequences
-    primers = set()
-    in_handle = open(primer_fasta, "rU")
-    reader = fastaReader(in_handle)
-    count = 0
-    for record in reader:
-        if rc:
-            seq = reverse_complement(record.sequence)
-        else:
-            seq = record.sequence
-        #primers.add(re.compile(make_reg_ex(seq)))
-        count += 1
-        for pattern in make_reg_ex_mm(seq, mm):
-            primers.add(pattern)
-    in_handle.close()
-    #Use set to avoid duplicates, sort to have longest first
-    #(so more specific primers found before less specific ones)
-    primers = sorted(set(primers), key=lambda p: -len(p))
-    return count, re.compile("|".join(primers)) #make one monster re!
-
-
-
-#Read primer file and record all specified sequences
-count, primer = load_primers_as_re(primer_fasta, mm, rc)
-print "%i primer sequences" % count
-
-short_neg = 0
-short_clipped = 0
-clipped = 0
-negs = 0
-
-if seq_format.lower()=="sff":
-    #SFF is different because we just change the trim points
-    if forward:
-        def process(records):
-            global short_clipped, short_neg, clipped, negs
-            for record in records:
-                left_clip = record.annotations["clip_qual_left"]
-                right_clip = record.annotations["clip_qual_right"]
-                seq = str(record.seq)[left_clip:right_clip].upper()
-                result = primer.search(seq)
-                if result:
-                    #Forward primer, take everything after it
-                    #so move the left clip along
-                    if len(seq) - result.end() >= min_len:
-                        record.annotations["clip_qual_left"] = left_clip + result.end()
-                        clipped += 1
-                        yield record
-                    else:
-                        short_clipped += 1
-                elif keep_negatives:
-                    if len(seq) >= min_len:
-                        negs += 1
-                        yield record
-                    else:
-                        short_neg += 1
-    else:
-        def process(records):
-            global short_clipped, short_neg, clipped, negs
-            for record in records:
-                left_clip = record.annotations["clip_qual_left"]
-                right_clip = record.annotations["clip_qual_right"]
-                seq = str(record.seq)[left_clip:right_clip].upper()
-                result = primer.search(seq)
-                if result:
-                    #Reverse primer, take everything before it
-                    #so move the right clip back
-                    new_len = result.start()
-                    if new_len >= min_len:
-                        record.annotations["clip_qual_right"] = left_clip + new_len
-                        clipped += 1
-                        yield record
-                    else:
-                        short_clipped += 1
-                elif keep_negatives:
-                    if len(seq) >= min_len:
-                        negs += 1
-                        yield record
-                    else:
-                        short_neg += 1
-    
-    in_handle = open(in_file, "rb")
-    try:
-        manifest = ReadRocheXmlManifest(in_handle)
-    except ValueError:
-        manifest = None
-    in_handle.seek(0)
-    out_handle = open(out_file, "wb")
-    writer = SffWriter(out_handle, xml=manifest)
-    writer.write_file(process(SffIterator(in_handle)))
-    #End of SFF code
-elif seq_format.lower().startswith("fastq"):
-    in_handle = open(in_file, "rU")
-    out_handle = open(out_file, "w")
-    reader = fastqReader(in_handle)
-    writer = fastqWriter(out_handle)
-    if forward:
-        for record in reader:
-            seq = record.sequence.upper()
-            result = primer.search(seq)
-            if result:
-                #Forward primer, take everything after it
-                cut = result.end()
-                record.sequence = seq[cut:]
-                if len(record.sequence) >= min_len:
-                    record.quality = record.quality[cut:]
-                    clipped += 1
-                    writer.write(record)
-                else:
-                    short_clipped += 1
-            elif keep_negatives:
-                if len(record) >= min_len:
-                    negs += 1
-                    writer.write(record)
-                else:
-                    short_negs += 1
-    else:
-        for record in reader:
-            seq = record.sequence.upper()
-            result = primer.search(seq)
-            if result:
-                #Reverse primer, take everything before it
-                cut = result.start()
-                record.sequence = seq[:cut]
-                if len(record.sequence) >= min_len:
-                    record.quality = record.quality[:cut]
-                    clipped += 1
-                    writer.write(record)
-                else:
-                    short_clipped += 1
-            elif keep_negatives:
-                if len(record) >= min_len:
-                    negs += 1
-                    writer.write(record)
-                else:
-                    short_negs += 1
-elif seq_format.lower()=="fasta":
-    in_handle = open(in_file, "rU")
-    out_handle = open(out_file, "w")
-    reader = fastaReader(in_handle)
-    writer = fastaWriter(out_handle)
-    #Following code is identical to that for FASTQ but without editing qualities
-    if forward:
-        for record in reader:
-            seq = record.sequence.upper()
-            result = primer.search(seq)
-            if result:
-                #Forward primer, take everything after it
-                cut = result.end()
-                record.sequence = seq[cut:]
-                if len(record.sequence) >= min_len:
-                    clipped += 1
-                    writer.write(record)
-                else:
-                    short_clipped += 1
-            elif keep_negatives:
-                if len(record) >= min_len:
-                    negs += 1
-                    writer.write(record)
-                else:
-                    short_negs += 1
-    else:
-        for record in reader:
-            seq = record.sequence.upper()
-            result = primer.search(seq)
-            if result:
-                #Reverse primer, take everything before it
-                cut = result.start()
-                record.sequence = seq[:cut]
-                if len(record.sequence) >= min_len:
-                    clipped += 1
-                    writer.write(record)
-                else:
-                    short_clipped += 1
-            elif keep_negatives:
-                if len(record) >= min_len:
-                    negs += 1
-                    writer.write(record)
-                else:
-                    short_negs += 1
-else:
-    stop_err("Unsupported file type %r" % seq_format)
-in_handle.close()
-out_handle.close()
-
-print "Kept %i clipped reads," % clipped
-print "discarded %i short." % short_clipped
-if keep_negatives:
-    print "Kept %i non-matching reads," % negs
-    print "discarded %i short." % short_neg
diff -r 8c02a91a8680 -r ee5acea162a7 tools/primers/seq_primer_clip.txt
--- a/tools/primers/seq_primer_clip.txt	Tue Apr 30 11:04:43 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,93 +0,0 @@
-Galaxy tool to primer clip (trim) FASTA, FASTQ or SFF reads
-===========================================================
-
-This tool is copyright 2011 by Peter Cock, The James Hutton Institute
-(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
-See the licence text below.
-
-This tool is a short Python script (using the Galaxy library functions and
-Biopython). There are just two files to install:
-
-* seq_primer_clip.py (the Python script)
-* seq_primer_clip.xml (the Galaxy tool definition)
-
-The suggested location is a new tools/primers folder. You will also need to
-modify the tools_conf.xml file to tell Galaxy to offer the tool:
-
-<tool file="primers/seq_primer_clip.xml" />
-
-If you wish to run the unit tests, also add this to tools_conf.xml.sample
-and move/copy the test-data files under Galaxy's test-data folder. Then:
-
-$ ./run_functional_tests.sh -id seq_primer_clip
-
-You will also need to install Biopython 1.54 or later. That's it.
-
-
-History
-=======
-
-v0.0.1 - Initial version (not publicly released)
-v0.0.2 - Sort primers by length (longest and therefore most specific first)
-v0.0.3 - Consider missing bases at start/end of read as mismatches
-v0.0.4 - Apply minimum length to sequences with no match too
-v0.0.5 - Count clipped & non-matched short reads separately, length bug fixes
-v0.0.6 - Added some functional tests
-v0.0.7 - Added error check for bad filename arguments
-v0.0.8 - Record version of Python script when run from Galaxy.
-       - Check for errors using Python script's return code.
-v0.0.9 - Moved test data to workaround Galaxy Tool Shed limititation.
-
-
-Developers
-==========
-
-This script and related tools are being developed on the following hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/tools
-
-This incorporates the previously used hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
-
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder:
-
-$ tar -czf seq_primer_clip.tar.gz tools/primers/seq_primer_clip.* test-data/dop_primers.fasta test-data/MID4_GLZRM4E04_rnd30*
-
-Check this worked:
-
-$ tar -tzf seq_primer_clip.tar.gz
-tools/primers/seq_primer_clip.py
-tools/primers/seq_primer_clip.txt
-tools/primers/seq_primer_clip.xml
-test-data/dop_primers.fasta
-test-data/MID4_GLZRM4E04_rnd30.fasta
-test-data/MID4_GLZRM4E04_rnd30.fastqsanger
-test-data/MID4_GLZRM4E04_rnd30_fclip.fasta
-test-data/MID4_GLZRM4E04_rnd30_fclip.fastqsanger
-test-data/MID4_GLZRM4E04_rnd30_fclip.sff
-test-data/MID4_GLZRM4E04_rnd30_frclip.fasta
-test-data/MID4_GLZRM4E04_rnd30_frclip.fastqsanger
-test-data/MID4_GLZRM4E04_rnd30_frclip.sff
-test-data/MID4_GLZRM4E04_rnd30.sff
-
-
-Licence (MIT/BSD style)
-=======================
-
-Permission to use, copy, modify, and distribute this software and its
-documentation with or without modifications and for any purpose and
-without fee is hereby granted, provided that any copyright notices
-appear in all copies and that both those copyright notices and this
-permission notice appear in supporting documentation, and that the
-names of the contributors or copyright holders not be used in
-advertising or publicity pertaining to distribution of the software
-without specific prior permission.
-
-THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
-WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
-CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
-OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
-OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
-OR PERFORMANCE OF THIS SOFTWARE.
diff -r 8c02a91a8680 -r ee5acea162a7 tools/primers/seq_primer_clip.txt.orig
--- a/tools/primers/seq_primer_clip.txt.orig	Tue Apr 30 11:04:43 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,103 +0,0 @@
-Galaxy tool to primer clip (trim) FASTA, FASTQ or SFF reads
-===========================================================
-
-This tool is copyright 2011 by Peter Cock, The James Hutton Institute
-(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
-See the licence text below.
-
-This tool is a short Python script (using the Galaxy library functions and
-Biopython). There are just two files to install:
-
-* seq_primer_clip.py (the Python script)
-* seq_primer_clip.xml (the Galaxy tool definition)
-
-The suggested location is a new tools/primers folder. You will also need to
-modify the tools_conf.xml file to tell Galaxy to offer the tool and also do
-this to tools_conf.xml.sample in order to run the tests:
-
-<tool file="primers/seq_primer_clip.xml" />
-
-There are optionally some example files required to run the functional tests,
-put these in the test-data/primers folder.
-
-test-data/primers/dop_primers.fasta
-test-data/primers/MID4_GLZRM4E04_rnd30.fasta
-test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger
-test-data/primers/MID4_GLZRM4E04_rnd30.sff
-test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta
-test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger
-test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff
-
-You should then be able to run the tests with:
-
-sh run_functional_tests.sh -id seq_primer_clip
-
-You will also need to install Biopython 1.54 or later. That's it.
-
-
-History
-=======
-
-v0.0.1 - Initial version (not publicly released)
-v0.0.2 - Sort primers by length (longest and therefore most specific first)
-v0.0.3 - Consider missing bases at start/end of read as mismatches
-v0.0.4 - Apply minimum length to sequences with no match too
-v0.0.5 - Count clipped & non-matched short reads separately, length bug fixes
-v0.0.6 - Added some functional tests
-v0.0.7 - Added error check for bad filename arguments
-v0.0.8 - Record version of Python script when run from Galaxy.
-       - Check for errors using Python script's return code.
-
-
-Developers
-==========
-
-This script and related tools are being developed on the following hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/tools
-
-This incorporates the previously used hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
-
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder:
-
-$ tar -czf seq_primer_clip.tar.gz tools/primers/seq_primer_clip.* test-data/primers/*
-
-Check this worked:
-
-$ tar -tzf seq_primer_clip.tar.gz
-tools/primers/seq_primer_clip.py
-tools/primers/seq_primer_clip.txt
-tools/primers/seq_primer_clip.xml
-test-data/primers/dop_primers.fasta
-test-data/primers/MID4_GLZRM4E04_rnd30.fasta
-test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger
-test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta
-test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger
-test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff
-test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fasta
-test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fastqsanger
-test-data/primers/MID4_GLZRM4E04_rnd30_frclip.sff
-test-data/primers/MID4_GLZRM4E04_rnd30.sff
-
-
-Licence (MIT/BSD style)
-=======================
-
-Permission to use, copy, modify, and distribute this software and its
-documentation with or without modifications and for any purpose and
-without fee is hereby granted, provided that any copyright notices
-appear in all copies and that both those copyright notices and this
-permission notice appear in supporting documentation, and that the
-names of the contributors or copyright holders not be used in
-advertising or publicity pertaining to distribution of the software
-without specific prior permission.
-
-THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
-WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
-CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
-OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
-OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
-OR PERFORMANCE OF THIS SOFTWARE.
diff -r 8c02a91a8680 -r ee5acea162a7 tools/primers/seq_primer_clip.xml
--- a/tools/primers/seq_primer_clip.xml	Tue Apr 30 11:04:43 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,137 +0,0 @@
-<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.9">
-    <description>Trim off 5' or 3' primers</description>
-    <version_command interpreter="python">seq_primer_clip.py --version</version_command>   
-    <command interpreter="python">
-seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file
-    </command>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <inputs>
-        <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to clip" description="FASTA, FASTQ, or SFF format."/>
-        <param name="primer_fasta" type="data" format="fasta" label="FASTA file containing primer(s)"/>
-        <param name="primer_type" type="select" label="Type of primers">
-            <option value="Forward">Forward (5') primers</option>
-            <option value="Reverse">Reverse (3') primers (given with respect to the forward strand)</option>
-            <option value="Reverse-complement">Reverse (3') primers (given with respect to the reverse strand)</option>
-        </param>
-        <param name="mm" type="integer" value="0" label="How many mismatches to allow? (0, 1 or 2)">
-            <validator type="in_range" min="0" max="2" />
-        </param>
-        <param name="keep_negatives" type="boolean" value="false" label="Keep reads with no matched primer"/>
-        <param name="min_len" type="integer" label="Minimum length for (clipped) sequences " value="1"/>
-    </inputs>
-    <outputs>
-        <data name="output_file" format="data" label="$primer_type primer clipped">
-            <!-- TODO - Replace this with format="input:input_fastq" if/when that works -->
-            <change_format>
-                <when input_dataset="input_file" attribute="extension" value="sff" format="sff" />
-                <when input_dataset="input_file" attribute="extension" value="fasta" format="fasta" />
-                <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" />
-                <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" />
-                <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" />
-                <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" />
-                <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" />
-            </change_format>
-        </data>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input_file" value="MID4_GLZRM4E04_rnd30.fasta" ftype="fasta" />
-            <param name="primer_fasta" value="dop_primers.fasta" />
-            <param name="primer_type" value="Forward" />
-            <param name="mm" value="2" />
-            <param name="keep_negatives" value="false" />
-            <param name="min_len" value="35" />
-            <output name="output_file" file="MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" />
-        </test>
-        <test>
-            <param name="input_file" value="MID4_GLZRM4E04_rnd30.fastqsanger" ftype="fastqsanger" />
-            <param name="primer_fasta" value="dop_primers.fasta" />
-            <param name="primer_type" value="Forward" />
-            <param name="mm" value="2" />
-            <param name="keep_negatives" value="false" />
-            <param name="min_len" value="35" />
-            <output name="output_file" file="MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" />
-        </test>
-        <test>
-            <param name="input_file" value="MID4_GLZRM4E04_rnd30.sff" ftype="sff" />
-            <param name="primer_fasta" value="dop_primers.fasta" />
-            <param name="primer_type" value="Forward" />
-            <param name="mm" value="2" />
-            <param name="keep_negatives" value="false" />
-            <param name="min_len" value="35" />
-            <output name="output_file" file="MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" />
-        </test>
-        <test>
-            <param name="input_file" value="MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" />
-            <param name="primer_fasta" value="dop_primers.fasta" />
-            <param name="primer_type" value="Reverse" />
-            <param name="mm" value="2" />
-            <param name="keep_negatives" value="true" />
-            <param name="min_len" value="35" />
-            <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.fasta" ftype="fasta" />
-        </test>
-        <test>
-            <param name="input_file" value="MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" />
-            <param name="primer_fasta" value="dop_primers.fasta" />
-            <param name="primer_type" value="Reverse" />
-            <param name="mm" value="2" />
-            <param name="keep_negatives" value="true" />
-            <param name="min_len" value="35" />
-            <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.fastqsanger" ftype="fastqsanger" />
-        </test>
-        <test>
-            <param name="input_file" value="MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" />
-            <param name="primer_fasta" value="dop_primers.fasta" />
-            <param name="primer_type" value="Reverse" />
-            <param name="mm" value="2" />
-            <param name="keep_negatives" value="true" />
-            <param name="min_len" value="35" />
-            <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" />
-        </test>
-    </tests>
-    <requirements>
-        <requirement type="python-module">Bio</requirement>
-    </requirements>
-    <help>
-
-**What it does**
-
-Looks for the given primer sequences (within the existing clipped sequence) and
-further clips the reads to remove the primers and any preceding/trailing sequence.
-
-Reads containing a forward primer are reduced to just the sequence after (and
-excluding) the forward primer.
-
-Reads containing a reverse primer are reduced to just the sequence before (and
-excluding) the reverse primer.
-
-Degenerate primers can be specified using the standard IUPAC ambiguity codes,
-thus a primer with an N would match A, C, T or G (or any of the IUPAC ambiguity
-codes) and so on.
-
-Note that for SFF files only the clip/trim positions are edited - you will still
-be able to extract the original full read (with any adapter sequence and poor
-quality sequence) if you need to.
-
-.. class:: warningmark
-
-**Note**. This tool was initially written for Roche 454 data, and should also
-work fine on Sanger or Ion Torrent as well. However, it is probably too slow
-for use on large Illumina datasets.
-
-
-**Citation**
-
-This tool uses Biopython. If you use this tool in scientific work leading to a
-publication, please cite:
-
-Cock et al 2009. Biopython: freely available Python tools for computational
-molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
-http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
-
-    </help>
-</tool>
diff -r 8c02a91a8680 -r ee5acea162a7 tools/primers/seq_primer_clip.xml.orig
--- a/tools/primers/seq_primer_clip.xml.orig	Tue Apr 30 11:04:43 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,137 +0,0 @@
-<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.8">
-    <description>Trim off 5' or 3' primers</description>
-    <version_command interpreter="python">seq_primer_clip.py --version</version_command>   
-    <command interpreter="python">
-seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file
-    </command>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <inputs>
-        <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to clip" description="FASTA, FASTQ, or SFF format."/>
-        <param name="primer_fasta" type="data" format="fasta" label="FASTA file containing primer(s)"/>
-        <param name="primer_type" type="select" label="Type of primers">
-            <option value="Forward">Forward (5') primers</option>
-            <option value="Reverse">Reverse (3') primers (given with respect to the forward strand)</option>
-            <option value="Reverse-complement">Reverse (3') primers (given with respect to the reverse strand)</option>
-        </param>
-        <param name="mm" type="integer" value="0" label="How many mismatches to allow? (0, 1 or 2)">
-            <validator type="in_range" min="0" max="2" />
-        </param>
-        <param name="keep_negatives" type="boolean" value="false" label="Keep reads with no matched primer"/>
-        <param name="min_len" type="integer" label="Minimum length for (clipped) sequences " value="1"/>
-    </inputs>
-    <outputs>
-        <data name="output_file" format="data" label="$primer_type primer clipped">
-            <!-- TODO - Replace this with format="input:input_fastq" if/when that works -->
-            <change_format>
-                <when input_dataset="input_file" attribute="extension" value="sff" format="sff" />
-                <when input_dataset="input_file" attribute="extension" value="fasta" format="fasta" />
-                <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" />
-                <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" />
-                <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" />
-                <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" />
-                <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" />
-            </change_format>
-        </data>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30.fasta" ftype="fasta" />
-            <param name="primer_fasta" value="primers/dop_primers.fasta" />
-            <param name="primer_type" value="Forward" />
-            <param name="mm" value="2" />
-            <param name="keep_negatives" value="false" />
-            <param name="min_len" value="35" />
-            <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" />
-        </test>
-        <test>
-            <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30.fastqsanger" ftype="fastqsanger" />
-            <param name="primer_fasta" value="primers/dop_primers.fasta" />
-            <param name="primer_type" value="Forward" />
-            <param name="mm" value="2" />
-            <param name="keep_negatives" value="false" />
-            <param name="min_len" value="35" />
-            <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" />
-        </test>
-        <test>
-            <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30.sff" ftype="sff" />
-            <param name="primer_fasta" value="primers/dop_primers.fasta" />
-            <param name="primer_type" value="Forward" />
-            <param name="mm" value="2" />
-            <param name="keep_negatives" value="false" />
-            <param name="min_len" value="35" />
-            <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" />
-        </test>
-        <test>
-            <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" />
-            <param name="primer_fasta" value="primers/dop_primers.fasta" />
-            <param name="primer_type" value="Reverse" />
-            <param name="mm" value="2" />
-            <param name="keep_negatives" value="true" />
-            <param name="min_len" value="35" />
-            <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_frclip.fasta" ftype="fasta" />
-        </test>
-        <test>
-            <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" />
-            <param name="primer_fasta" value="primers/dop_primers.fasta" />
-            <param name="primer_type" value="Reverse" />
-            <param name="mm" value="2" />
-            <param name="keep_negatives" value="true" />
-            <param name="min_len" value="35" />
-            <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_frclip.fastqsanger" ftype="fastqsanger" />
-        </test>
-        <test>
-            <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" />
-            <param name="primer_fasta" value="primers/dop_primers.fasta" />
-            <param name="primer_type" value="Reverse" />
-            <param name="mm" value="2" />
-            <param name="keep_negatives" value="true" />
-            <param name="min_len" value="35" />
-            <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" />
-        </test>
-    </tests>
-    <requirements>
-        <requirement type="python-module">Bio</requirement>
-    </requirements>
-    <help>
-
-**What it does**
-
-Looks for the given primer sequences (within the existing clipped sequence) and
-further clips the reads to remove the primers and any preceding/trailing sequence.
-
-Reads containing a forward primer are reduced to just the sequence after (and
-excluding) the forward primer.
-
-Reads containing a reverse primer are reduced to just the sequence before (and
-excluding) the reverse primer.
-
-Degenerate primers can be specified using the standard IUPAC ambiguity codes,
-thus a primer with an N would match A, C, T or G (or any of the IUPAC ambiguity
-codes) and so on.
-
-Note that for SFF files only the clip/trim positions are edited - you will still
-be able to extract the original full read (with any adapter sequence and poor
-quality sequence) if you need to.
-
-.. class:: warningmark
-
-**Note**. This tool was initially written for Roche 454 data, and should also
-work fine on Sanger or Ion Torrent as well. However, it is probably too slow
-for use on large Illumina datasets.
-
-
-**Citation**
-
-This tool uses Biopython. If you use this tool in scientific work leading to a
-publication, please cite:
-
-Cock et al 2009. Biopython: freely available Python tools for computational
-molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
-http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
-
-    </help>
-</tool>
diff -r 8c02a91a8680 -r ee5acea162a7 tools/seq_primer_clip/README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/seq_primer_clip/README.rst	Thu Oct 24 09:37:25 2013 -0400
@@ -0,0 +1,120 @@
+Galaxy tool to primer clip (trim) FASTA, FASTQ or SFF reads
+===========================================================
+
+This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below (MIT licence).
+
+This tool is a short Python script (using the Galaxy library functions and
+Biopython). It is available from the Galaxy Tool Shed here:
+http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip
+
+
+Automated Installation
+======================
+
+This should be straightforward using the Galaxy Tool Shed, which should be
+able to automatically install the dependency on Biopython, and then install
+this tool and run its unit tests.
+
+
+Manual Installation
+===================
+
+There are just two files to install:
+
+* seq_primer_clip.py (the Python script)
+* seq_primer_clip.xml (the Galaxy tool definition)
+
+The suggested location is a new tools/seq_primer_clip folder. You will also
+need to modify the tools_conf.xml file to tell Galaxy to offer the tool::
+
+  <tool file="seq_primer_clip/seq_primer_clip.xml" />
+
+If you wish to run the unit tests, also add this to tools_conf.xml.sample
+and move/copy the test-data files under Galaxy's test-data folder. Then::
+
+    $ ./run_functional_tests.sh -id seq_primer_clip
+
+You will also need to install Biopython 1.54 or later. That's it.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial version (not publicly released)
+v0.0.2  - Sort primers by length (longest and therefore most specific first)
+v0.0.3  - Consider missing bases at start/end of read as mismatches
+v0.0.4  - Apply minimum length to sequences with no match too
+v0.0.5  - Count clipped & non-matched short reads separately, length bug fixes
+v0.0.6  - Added some functional tests
+v0.0.7  - Added error check for bad filename arguments
+v0.0.8  - Record version of Python script when run from Galaxy.
+        - Check for errors using Python script's return code.
+v0.0.9  - Moved test data to workaround Galaxy Tool Shed limititation.
+v0.0.10 - Include links to Tool Shed in help text and this README file.
+        - Use reStructuredText for this README file.
+        - Adopted standard MIT licence.
+        - Automated installation of Biopython dependency.
+        - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
+        - Renamed folder and adopted README.rst naming.
+======= ======================================================================
+
+
+Developers
+==========
+
+This script and related tools were initially developed on the following hg branches:
+http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
+http://bitbucket.org/peterjc/galaxy-central/src/tools
+
+Development has now moved to a dedicated GitHub repository:
+https://github.com/peterjc/pico_galaxy
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder::
+
+    $ tar -czf seq_primer_clip.tar.gz tools/seq_primer_clip/README.rst tools/seq_primer_clip/seq_primer_clip.* tools/seq_primer_clip/repository_dependencies.xml test-data/dop_primers.fasta test-data/MID4_GLZRM4E04_rnd30*
+
+Check this worked::
+
+    $ tar -tzf seq_primer_clip.tar.gz
+    tools/seq_primer_clip/README.rst
+    tools/seq_primer_clip/seq_primer_clip.xml
+    tools/seq_primer_clip/seq_primer_clip.py
+    tools/seq_primer_clip/repository_dependencies.xml
+    test-data/dop_primers.fasta
+    test-data/MID4_GLZRM4E04_rnd30.fasta
+    test-data/MID4_GLZRM4E04_rnd30.fastqsanger
+    test-data/MID4_GLZRM4E04_rnd30_fclip.fasta
+    test-data/MID4_GLZRM4E04_rnd30_fclip.fastqsanger
+    test-data/MID4_GLZRM4E04_rnd30_fclip.sff
+    test-data/MID4_GLZRM4E04_rnd30_frclip.fasta
+    test-data/MID4_GLZRM4E04_rnd30_frclip.fastqsanger
+    test-data/MID4_GLZRM4E04_rnd30_frclip.sff
+    test-data/MID4_GLZRM4E04_rnd30.sff
+
+
+Licence (MIT)
+=============
+
+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.
diff -r 8c02a91a8680 -r ee5acea162a7 tools/seq_primer_clip/repository_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/seq_primer_clip/repository_dependencies.xml	Thu Oct 24 09:37:25 2013 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<repositories description="This requires Biopython as a dependency.">
+<!-- Leave out the tool shed and revision to get the current
+     tool shed and latest revision at the time of upload -->
+<repository changeset_revision="3e82cbc44886" name="package_biopython_1_62" owner="biopython" toolshed="http://toolshed.g2.bx.psu.edu" />
+</repositories>
diff -r 8c02a91a8680 -r ee5acea162a7 tools/seq_primer_clip/seq_primer_clip.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/seq_primer_clip/seq_primer_clip.py	Thu Oct 24 09:37:25 2013 -0400
@@ -0,0 +1,358 @@
+#!/usr/bin/env python
+"""Looks for the given primer sequences and clips matching SFF reads.
+
+Takes eight command line options, input read filename, input read format,
+input primer FASTA filename, type of primers (forward, reverse or reverse-
+complement), number of mismatches (currently only 0, 1 and 2 are supported),
+minimum length to keep a read (after primer trimming), should primer-less
+reads be kept (boolean), and finally the output sequence filename.
+
+Both the primer and read sequences can contain IUPAC ambiguity codes like N.
+
+This supports FASTA, FASTQ and SFF sequence files. Colorspace reads are not
+supported.
+
+The mismatch parameter does not consider gapped alignemnts, however the
+special case of missing bases at the very start or end of the read is handled.
+e.g. a primer sequence CCGACTCGAG will match a read starting CGACTCGAG...
+if one or more mismatches are allowed.
+
+This can also be used for stripping off (and optionally filtering on) barcodes.
+
+Note that only the trim/clip values in the SFF file are changed, not the flow
+information of the full read sequence.
+
+This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute
+(formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved.
+See accompanying text file for licence details (MIT/BSD style).
+
+This is version 0.0.8 of the script. Currently it uses Python's regular
+expression engine for finding the primers, which for my needs is fast enough.
+"""
+import sys
+import re
+from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
+from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
+
+if "-v" in sys.argv or "--version" in sys.argv:
+    print "v0.0.5"
+    sys.exit(0)
+
+def stop_err(msg, err=1):
+    sys.stderr.write(msg)
+    sys.exit(err)
+
+try:
+    from Bio.Seq import reverse_complement
+    from Bio.SeqIO.SffIO import SffIterator, SffWriter
+except ImportError:
+    stop_err("Requires Biopython 1.54 or later")
+try:
+    from Bio.SeqIO.SffIO import ReadRocheXmlManifest
+except ImportError:
+    #Prior to Biopython 1.56 this was a private function
+    from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest
+
+#Parse Command Line
+try:
+    in_file, seq_format, primer_fasta, primer_type, mm, min_len, keep_negatives, out_file = sys.argv[1:]
+except ValueError:
+    stop_err("Expected 8 arguments, got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv)))
+
+if in_file == primer_fasta:
+    stop_err("Same file given as both primer sequences and sequences to clip!")
+if in_file == out_file:
+    stop_err("Same file given as both sequences to clip and output!")
+if primer_fasta == out_file:
+    stop_err("Same file given as both primer sequences and output!")
+
+try:
+    mm = int(mm)
+except ValueError:
+    stop_err("Expected non-negative integer number of mismatches (e.g. 0 or 1), not %r" % mm)
+if mm < 0:
+    stop_err("Expected non-negtive integer number of mismatches (e.g. 0 or 1), not %r" % mm)
+if mm not in [0,1,2]:
+    raise NotImplementedError
+
+try:
+    min_len = int(min_len)
+except ValueError:
+    stop_err("Expected non-negative integer min_len (e.g. 0 or 1), not %r" % min_len)
+if min_len < 0:
+    stop_err("Expected non-negtive integer min_len (e.g. 0 or 1), not %r" % min_len)
+
+
+if keep_negatives.lower() in ["true", "yes", "on"]:
+    keep_negatives = True
+elif keep_negatives.lower() in ["false", "no", "off"]:
+    keep_negatives = False
+else:
+    stop_err("Expected boolean for keep_negatives (e.g. true or false), not %r" % keep_negatives)
+
+
+if primer_type.lower() == "forward":
+    forward = True
+    rc = False
+elif primer_type.lower() == "reverse":
+    forward = False
+    rc = False
+elif primer_type.lower() == "reverse-complement":
+    forward = False
+    rc = True
+else:
+    stop_err("Expected foward, reverse or reverse-complement not %r" % primer_type)
+
+
+ambiguous_dna_values = {
+    "A": "A",
+    "C": "C",
+    "G": "G",
+    "T": "T",
+    "M": "ACM",
+    "R": "AGR",
+    "W": "ATW",
+    "S": "CGS",
+    "Y": "CTY",
+    "K": "GTK",
+    "V": "ACGMRSV",
+    "H": "ACTMWYH",
+    "D": "AGTRWKD",
+    "B": "CGTSYKB",
+    "X": ".", #faster than [GATCMRWSYKVVHDBXN] or even [GATC]
+    "N": ".",
+    }
+
+ambiguous_dna_re = {}
+for letter, values in ambiguous_dna_values.iteritems():
+    if len(values) == 1:
+        ambiguous_dna_re[letter] = values
+    else:
+        ambiguous_dna_re[letter] = "[%s]" % values
+
+
+def make_reg_ex(seq):
+    return "".join(ambiguous_dna_re[letter] for letter in seq)
+
+def make_reg_ex_mm(seq, mm):
+    if mm > 2:
+        raise NotImplementedError("At most 2 mismatches allowed!")
+    seq = seq.upper()
+    yield make_reg_ex(seq)
+    for i in range(1,mm+1):
+        #Missing first/last i bases at very start/end of sequence
+        for reg in make_reg_ex_mm(seq[i:],  mm-i):
+            yield "^" + reg
+        for reg in make_reg_ex_mm(seq[:-i], mm-i):
+            yield "$" + reg
+    if mm >= 1:
+        for i,letter in enumerate(seq):
+            #We'll use a set to remove any duplicate patterns
+            #if letter not in "NX":
+            pattern = seq[:i] + "N" + seq[i+1:]
+            assert len(pattern) == len(seq), "Len %s is %i, len %s is %i" \
+                   % (pattern, len(pattern), seq, len(seq))
+            yield make_reg_ex(pattern)
+    if mm >=2:
+        for i,letter in enumerate(seq):
+            #We'll use a set to remove any duplicate patterns
+            #if letter not in "NX":
+            for k,letter in enumerate(seq[i+1:]):
+                #We'll use a set to remove any duplicate patterns
+                #if letter not in "NX":
+                pattern = seq[:i] + "N" + seq[i+1:i+1+k] + "N" + seq[i+k+2:]
+                assert len(pattern) == len(seq), "Len %s is %i, len %s is %i" \
+                       % (pattern, len(pattern), seq, len(seq))
+                yield make_reg_ex(pattern)
+
+def load_primers_as_re(primer_fasta, mm, rc=False):
+    #Read primer file and record all specified sequences
+    primers = set()
+    in_handle = open(primer_fasta, "rU")
+    reader = fastaReader(in_handle)
+    count = 0
+    for record in reader:
+        if rc:
+            seq = reverse_complement(record.sequence)
+        else:
+            seq = record.sequence
+        #primers.add(re.compile(make_reg_ex(seq)))
+        count += 1
+        for pattern in make_reg_ex_mm(seq, mm):
+            primers.add(pattern)
+    in_handle.close()
+    #Use set to avoid duplicates, sort to have longest first
+    #(so more specific primers found before less specific ones)
+    primers = sorted(set(primers), key=lambda p: -len(p))
+    return count, re.compile("|".join(primers)) #make one monster re!
+
+
+
+#Read primer file and record all specified sequences
+count, primer = load_primers_as_re(primer_fasta, mm, rc)
+print "%i primer sequences" % count
+
+short_neg = 0
+short_clipped = 0
+clipped = 0
+negs = 0
+
+if seq_format.lower()=="sff":
+    #SFF is different because we just change the trim points
+    if forward:
+        def process(records):
+            global short_clipped, short_neg, clipped, negs
+            for record in records:
+                left_clip = record.annotations["clip_qual_left"]
+                right_clip = record.annotations["clip_qual_right"]
+                seq = str(record.seq)[left_clip:right_clip].upper()
+                result = primer.search(seq)
+                if result:
+                    #Forward primer, take everything after it
+                    #so move the left clip along
+                    if len(seq) - result.end() >= min_len:
+                        record.annotations["clip_qual_left"] = left_clip + result.end()
+                        clipped += 1
+                        yield record
+                    else:
+                        short_clipped += 1
+                elif keep_negatives:
+                    if len(seq) >= min_len:
+                        negs += 1
+                        yield record
+                    else:
+                        short_neg += 1
+    else:
+        def process(records):
+            global short_clipped, short_neg, clipped, negs
+            for record in records:
+                left_clip = record.annotations["clip_qual_left"]
+                right_clip = record.annotations["clip_qual_right"]
+                seq = str(record.seq)[left_clip:right_clip].upper()
+                result = primer.search(seq)
+                if result:
+                    #Reverse primer, take everything before it
+                    #so move the right clip back
+                    new_len = result.start()
+                    if new_len >= min_len:
+                        record.annotations["clip_qual_right"] = left_clip + new_len
+                        clipped += 1
+                        yield record
+                    else:
+                        short_clipped += 1
+                elif keep_negatives:
+                    if len(seq) >= min_len:
+                        negs += 1
+                        yield record
+                    else:
+                        short_neg += 1
+    
+    in_handle = open(in_file, "rb")
+    try:
+        manifest = ReadRocheXmlManifest(in_handle)
+    except ValueError:
+        manifest = None
+    in_handle.seek(0)
+    out_handle = open(out_file, "wb")
+    writer = SffWriter(out_handle, xml=manifest)
+    writer.write_file(process(SffIterator(in_handle)))
+    #End of SFF code
+elif seq_format.lower().startswith("fastq"):
+    in_handle = open(in_file, "rU")
+    out_handle = open(out_file, "w")
+    reader = fastqReader(in_handle)
+    writer = fastqWriter(out_handle)
+    if forward:
+        for record in reader:
+            seq = record.sequence.upper()
+            result = primer.search(seq)
+            if result:
+                #Forward primer, take everything after it
+                cut = result.end()
+                record.sequence = seq[cut:]
+                if len(record.sequence) >= min_len:
+                    record.quality = record.quality[cut:]
+                    clipped += 1
+                    writer.write(record)
+                else:
+                    short_clipped += 1
+            elif keep_negatives:
+                if len(record) >= min_len:
+                    negs += 1
+                    writer.write(record)
+                else:
+                    short_negs += 1
+    else:
+        for record in reader:
+            seq = record.sequence.upper()
+            result = primer.search(seq)
+            if result:
+                #Reverse primer, take everything before it
+                cut = result.start()
+                record.sequence = seq[:cut]
+                if len(record.sequence) >= min_len:
+                    record.quality = record.quality[:cut]
+                    clipped += 1
+                    writer.write(record)
+                else:
+                    short_clipped += 1
+            elif keep_negatives:
+                if len(record) >= min_len:
+                    negs += 1
+                    writer.write(record)
+                else:
+                    short_negs += 1
+elif seq_format.lower()=="fasta":
+    in_handle = open(in_file, "rU")
+    out_handle = open(out_file, "w")
+    reader = fastaReader(in_handle)
+    writer = fastaWriter(out_handle)
+    #Following code is identical to that for FASTQ but without editing qualities
+    if forward:
+        for record in reader:
+            seq = record.sequence.upper()
+            result = primer.search(seq)
+            if result:
+                #Forward primer, take everything after it
+                cut = result.end()
+                record.sequence = seq[cut:]
+                if len(record.sequence) >= min_len:
+                    clipped += 1
+                    writer.write(record)
+                else:
+                    short_clipped += 1
+            elif keep_negatives:
+                if len(record) >= min_len:
+                    negs += 1
+                    writer.write(record)
+                else:
+                    short_negs += 1
+    else:
+        for record in reader:
+            seq = record.sequence.upper()
+            result = primer.search(seq)
+            if result:
+                #Reverse primer, take everything before it
+                cut = result.start()
+                record.sequence = seq[:cut]
+                if len(record.sequence) >= min_len:
+                    clipped += 1
+                    writer.write(record)
+                else:
+                    short_clipped += 1
+            elif keep_negatives:
+                if len(record) >= min_len:
+                    negs += 1
+                    writer.write(record)
+                else:
+                    short_negs += 1
+else:
+    stop_err("Unsupported file type %r" % seq_format)
+in_handle.close()
+out_handle.close()
+
+print "Kept %i clipped reads," % clipped
+print "discarded %i short." % short_clipped
+if keep_negatives:
+    print "Kept %i non-matching reads," % negs
+    print "discarded %i short." % short_neg
diff -r 8c02a91a8680 -r ee5acea162a7 tools/seq_primer_clip/seq_primer_clip.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/seq_primer_clip/seq_primer_clip.xml	Thu Oct 24 09:37:25 2013 -0400
@@ -0,0 +1,143 @@
+<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.10">
+    <description>Trim off 5' or 3' primers</description>
+    <requirements>
+        <requirement type="package" version="1.62">biopython</requirement>
+        <requirement type="python-module">Bio</requirement>
+    </requirements>
+    <version_command interpreter="python">seq_primer_clip.py --version</version_command>   
+    <command interpreter="python">
+seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file
+    </command>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <inputs>
+        <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to clip" description="FASTA, FASTQ, or SFF format."/>
+        <param name="primer_fasta" type="data" format="fasta" label="FASTA file containing primer(s)"/>
+        <param name="primer_type" type="select" label="Type of primers">
+            <option value="Forward">Forward (5') primers</option>
+            <option value="Reverse">Reverse (3') primers (given with respect to the forward strand)</option>
+            <option value="Reverse-complement">Reverse (3') primers (given with respect to the reverse strand)</option>
+        </param>
+        <param name="mm" type="integer" value="0" label="How many mismatches to allow? (0, 1 or 2)">
+            <validator type="in_range" min="0" max="2" />
+        </param>
+        <param name="keep_negatives" type="boolean" value="false" label="Keep reads with no matched primer"/>
+        <param name="min_len" type="integer" label="Minimum length for (clipped) sequences " value="1"/>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="data" label="$primer_type primer clipped">
+            <!-- TODO - Replace this with format="input:input_fastq" if/when that works -->
+            <change_format>
+                <when input_dataset="input_file" attribute="extension" value="sff" format="sff" />
+                <when input_dataset="input_file" attribute="extension" value="fasta" format="fasta" />
+                <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" />
+                <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" />
+                <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" />
+                <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" />
+                <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="MID4_GLZRM4E04_rnd30.fasta" ftype="fasta" />
+            <param name="primer_fasta" value="dop_primers.fasta" />
+            <param name="primer_type" value="Forward" />
+            <param name="mm" value="2" />
+            <param name="keep_negatives" value="false" />
+            <param name="min_len" value="35" />
+            <output name="output_file" file="MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" />
+        </test>
+        <test>
+            <param name="input_file" value="MID4_GLZRM4E04_rnd30.fastqsanger" ftype="fastqsanger" />
+            <param name="primer_fasta" value="dop_primers.fasta" />
+            <param name="primer_type" value="Forward" />
+            <param name="mm" value="2" />
+            <param name="keep_negatives" value="false" />
+            <param name="min_len" value="35" />
+            <output name="output_file" file="MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" />
+        </test>
+        <test>
+            <param name="input_file" value="MID4_GLZRM4E04_rnd30.sff" ftype="sff" />
+            <param name="primer_fasta" value="dop_primers.fasta" />
+            <param name="primer_type" value="Forward" />
+            <param name="mm" value="2" />
+            <param name="keep_negatives" value="false" />
+            <param name="min_len" value="35" />
+            <output name="output_file" file="MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" />
+        </test>
+        <test>
+            <param name="input_file" value="MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" />
+            <param name="primer_fasta" value="dop_primers.fasta" />
+            <param name="primer_type" value="Reverse" />
+            <param name="mm" value="2" />
+            <param name="keep_negatives" value="true" />
+            <param name="min_len" value="35" />
+            <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.fasta" ftype="fasta" />
+        </test>
+        <test>
+            <param name="input_file" value="MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" />
+            <param name="primer_fasta" value="dop_primers.fasta" />
+            <param name="primer_type" value="Reverse" />
+            <param name="mm" value="2" />
+            <param name="keep_negatives" value="true" />
+            <param name="min_len" value="35" />
+            <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.fastqsanger" ftype="fastqsanger" />
+        </test>
+        <test>
+            <param name="input_file" value="MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" />
+            <param name="primer_fasta" value="dop_primers.fasta" />
+            <param name="primer_type" value="Reverse" />
+            <param name="mm" value="2" />
+            <param name="keep_negatives" value="true" />
+            <param name="min_len" value="35" />
+            <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" />
+        </test>
+    </tests>
+    <requirements>
+        <requirement type="python-module">Bio</requirement>
+    </requirements>
+    <help>
+
+**What it does**
+
+Looks for the given primer sequences (within the existing clipped sequence) and
+further clips the reads to remove the primers and any preceding/trailing sequence.
+
+Reads containing a forward primer are reduced to just the sequence after (and
+excluding) the forward primer.
+
+Reads containing a reverse primer are reduced to just the sequence before (and
+excluding) the reverse primer.
+
+Degenerate primers can be specified using the standard IUPAC ambiguity codes,
+thus a primer with an N would match A, C, T or G (or any of the IUPAC ambiguity
+codes) and so on.
+
+Note that for SFF files only the clip/trim positions are edited - you will still
+be able to extract the original full read (with any adapter sequence and poor
+quality sequence) if you need to.
+
+.. class:: warningmark
+
+**Note**. This tool was initially written for Roche 454 data, and should also
+work fine on Sanger or Ion Torrent as well. However, it is probably too slow
+for use on large Illumina datasets.
+
+
+**Citation**
+
+This tool uses Biopython. If you use this tool in scientific work leading to a
+publication, please cite:
+
+Cock et al 2009. Biopython: freely available Python tools for computational
+molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
+http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
+
+This tool is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip 
+    </help>
+</tool>