Mercurial > repos > lparsons > cutadapt
changeset 3:7ed26fc9fa8a
Updated for cutadapt 0.9.4, no longer need python wrapper
| author | Lance Parsons <lparsons@princeton.edu> |
|---|---|
| date | Wed, 25 May 2011 18:54:09 -0400 |
| parents | f6b94b76d16b |
| children | 0a872e59164c |
| files | cutadapt.xml cutadapt_galaxy_wrapper.py |
| diffstat | 2 files changed, 14 insertions(+), 5 deletions(-) [+] |
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--- 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>
--- 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: