# HG changeset patch
# User Lance Parsons <lparsons@princeton.edu>
# Date 1306364049 14400
# Node ID 7ed26fc9fa8a7c1b3c14d29e0decb3ca7cbbc9f5
# Parent  f6b94b76d16b5230b92fe303825a862631e2c8b0
Updated for cutadapt 0.9.4, no longer need python wrapper

diff -r f6b94b76d16b -r 7ed26fc9fa8a cutadapt.xml
--- a/cutadapt.xml	Mon May 16 16:34:09 2011 -0400
+++ b/cutadapt.xml	Wed May 25 18:54:09 2011 -0400
@@ -1,10 +1,10 @@
-<tool id="cutadapt" name="Remove adapter sequences" version="0.9.3">
+<tool id="cutadapt" name="Remove adapter sequences" version="0.9.4">
 	<description>from high-throughput sequence data</description>
 	<requirements>
 		<requirement type="python-module">cutadapt</requirement>
 	</requirements>
 
-	<command interpreter="python">cutadapt_galaxy_wrapper.py 
+	<command>cutadapt 
 		#if $input.extension.startswith( "fastq"):
 		--format=fastq
 		#else
@@ -25,9 +25,12 @@
 		#if str($max) != '0':
 		-M $max
 		#end if
-		--input='$input'
+		#if $discard:
+		--discard
+		#end if
+		'$input'
 		--output='$output' 
-		> $report
+		2> $report
 	</command>
 	<inputs>
 		<param format="fastqsanger, fasta" name="input" type="data" optional="false" label="Fastq file to trim" length="100"/>
@@ -78,7 +81,7 @@
 		<param name="error_rate" type="float" min="0" max="1" value="0.1" label="Maximum error rate" help="Maximum allowed error rate (no. of errors divided by the length of the matching region)." />
 		<param name="count" type="integer" min="1" value="1" label="Match times" help="Try to remove adapters at most COUNT times. Useful when an adapter gets appended multiple times." />
 		<param name="overlap" type="integer" min="1" value="3" label="Minimum overlap length" help="Minimum overlap length. If the overlap between the adapter and the sequence is shorter than LENGTH, the read is not modified." />
-		<!--<param name="discard" type="boolean" checked="false" label="Discard Trimmed Reads" help="Discard reads that contain the adapter instead of trimming them. Use the 'Minimum overlap length' option in order to avoid throwing away too many randomly matching reads!" />-->
+		<param name="discard" type="boolean" checked="False" default="False" label="Discard Trimmed Reads" help="Discard reads that contain the adapter instead of trimming them. Use the 'Minimum overlap length' option in order to avoid throwing away too many randomly matching reads!" />
 		<param name="min" type="integer" min="0" optional="true" value="0" label="Minimum length" help="Discard trimmed reads that are shorter than LENGTH.  Reads that are too short even before adapter removal are also discarded. In colorspace, an initial primer is not counted. Value of 0 means no minimum length." />
 		<param name="max" type="integer" min="0" optional="true" value="0" label="Maximum length" help="Discard trimmed reads that are longer than LENGTH.  Reads that are too long even before adapter removal are also discarded. In colorspace, an initial primer is not counted. Value of 0 means no maximum length." />
 	</inputs>
diff -r f6b94b76d16b -r 7ed26fc9fa8a cutadapt_galaxy_wrapper.py
--- a/cutadapt_galaxy_wrapper.py	Mon May 16 16:34:09 2011 -0400
+++ b/cutadapt_galaxy_wrapper.py	Wed May 25 18:54:09 2011 -0400
@@ -14,6 +14,7 @@
         [--discard discard trimmed reads]
         [-m minimum read length]
         [-M maximum read length]
+        [-q quality cutoff]
         [-h,--help] [-v,--verbose] [--version]
 
 DESCRIPTION
@@ -64,6 +65,9 @@
         params.append("-m %s" % options.minimum_length)
     if options.maximum_length != None:
         params.append("-M %s" % options.maximum_length)
+    if options.cutoff != None:
+        params.append("-q %s" % options.cutoff)
+
 
     # cutadapt relies on the extension to determine file format: .fasta or .fastq
     input_name = '.'.join((options.input,options.format))
@@ -107,6 +111,8 @@
         parser.add_option ('--discard', '--discard-trimmed', dest='discard_trimmed', action='store_true', default=False, help='Discard reads that contain the adapter')
         parser.add_option ('-m', '--minimum-length', dest='minimum_length', help='Discard reads that are shorter than LENGTH')
         parser.add_option ('-M', '--maximum-length', dest='maximum_length', help='Discard reads that are longer than LENGTH')
+        parser.add_option ('-q', '--quality-cutoff', dest='cutoff', help='Trim
+                           low quality ends from reads before adapter removal')
         parser.add_option ('-o', '--output', dest='output_file', help='The modified sequences are written to the file')
         (options, args) = parser.parse_args()
         if options.input == None: