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comparison cutadapt.xml @ 3:7ed26fc9fa8a

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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
comparison
equal deleted inserted replaced
2:f6b94b76d16b 3:7ed26fc9fa8a
1 <tool id="cutadapt" name="Remove adapter sequences" version="0.9.3"> 1 <tool id="cutadapt" name="Remove adapter sequences" version="0.9.4">
2 <description>from high-throughput sequence data</description> 2 <description>from high-throughput sequence data</description>
3 <requirements> 3 <requirements>
4 <requirement type="python-module">cutadapt</requirement> 4 <requirement type="python-module">cutadapt</requirement>
5 </requirements> 5 </requirements>
6 6
7 <command interpreter="python">cutadapt_galaxy_wrapper.py 7 <command>cutadapt
8 #if $input.extension.startswith( "fastq"): 8 #if $input.extension.startswith( "fastq"):
9 --format=fastq 9 --format=fastq
10 #else 10 #else
11 --format=$input.extension 11 --format=$input.extension
12 #end if 12 #end if
23 -m $min 23 -m $min
24 #end if 24 #end if
25 #if str($max) != '0': 25 #if str($max) != '0':
26 -M $max 26 -M $max
27 #end if 27 #end if
28 --input='$input' 28 #if $discard:
29 --discard
30 #end if
31 '$input'
29 --output='$output' 32 --output='$output'
30 > $report 33 2> $report
31 </command> 34 </command>
32 <inputs> 35 <inputs>
33 <param format="fastqsanger, fasta" name="input" type="data" optional="false" label="Fastq file to trim" length="100"/> 36 <param format="fastqsanger, fasta" name="input" type="data" optional="false" label="Fastq file to trim" length="100"/>
34 37
35 <repeat name="adapters" title="3' Adapters"> 38 <repeat name="adapters" title="3' Adapters">
76 </repeat> 79 </repeat>
77 80
78 <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)." /> 81 <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)." />
79 <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." /> 82 <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." />
80 <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." /> 83 <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." />
81 <!--<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!" />--> 84 <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!" />
82 <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." /> 85 <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." />
83 <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." /> 86 <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." />
84 </inputs> 87 </inputs>
85 <outputs> 88 <outputs>
86 <data format="txt" name="report" label="${tool.name} on ${on_string} (Report)" /> 89 <data format="txt" name="report" label="${tool.name} on ${on_string} (Report)" />