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comparison trim_galore_wrapper.xml @ 2:9109c2c3be1e draft

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author bgruening
date Fri, 19 Jul 2013 09:37:45 -0400
parents 898db63d2e84
children eb546ac2aab2
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1:898db63d2e84 2:9109c2c3be1e
2 <!-- Wrapper compatible with Trim Galore version 0.2.8 --> 2 <!-- Wrapper compatible with Trim Galore version 0.2.8 -->
3 <description>adaptive quality and adapter trimmer</description> 3 <description>adaptive quality and adapter trimmer</description>
4 <version_command interpreter="perl">trim_galore --version</version_command> 4 <version_command interpreter="perl">trim_galore --version</version_command>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="1.1">cutadapt</requirement> 6 <requirement type="package" version="1.1">cutadapt</requirement>
7 <requirement type="package" version="0.10.1">fastqc</requirement>
8 </requirements> 7 </requirements>
9 <command interpreter="perl"> 8 <command interpreter="perl">
10 #from glob import glob 9 #from glob import glob
11 #import tempfile, os 10 #import tempfile, os
12 11
47 ## 46 ##
48 47
49 48
50 #if $params.settingsType == "custom": 49 #if $params.settingsType == "custom":
51 50
52 $params.fastqc
53 ## default 20 51 ## default 20
54 --quality $params.quality 52 --quality $params.quality
55 ## default 'AGATCGGAAGAGC' 53 ## default 'AGATCGGAAGAGC'
56 #if $params.adapter.strip() != '': 54 #if $params.adapter.strip() != '':
57 --adapter $params.adapter 55 --adapter $params.adapter
176 174
177 #end if 175 #end if
178 #end if 176 #end if
179 177
180 ## delete the temp_dir 178 ## delete the temp_dir
181 ##rm -rf $temp_dir 179 rm -rf $temp_dir
182 180
183 </command> 181 </command>
184 <inputs> 182 <inputs>
185 183
186 <!-- Input Parameters --> 184 <!-- Input Parameters -->
209 <option value="custom">Full parameter list</option> 207 <option value="custom">Full parameter list</option>
210 </param> 208 </param>
211 <when value="default" /> 209 <when value="default" />
212 <!-- Full/advanced params. --> 210 <!-- Full/advanced params. -->
213 <when value="custom"> 211 <when value="custom">
214 <param name="fastqc" type="boolean" truevalue="--fastqc" falsevalue="" checked="False" label="Run FastQC in the default mode on the FastQ file once trimming is complete" help="" />
215 <param name="quality" type="integer" value="20" label="Trim low-quality ends from reads in addition to adapter removal." help="For more information please see below." /> 212 <param name="quality" type="integer" value="20" label="Trim low-quality ends from reads in addition to adapter removal." help="For more information please see below." />
216 <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed"> 213 <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed">
217 <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator> 214 <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
218 </param> 215 </param>
219 <param name="stringency" type="integer" value="1" label="Overlap with adapter sequence required to trim a sequence" /> 216 <param name="stringency" type="integer" value="1" label="Overlap with adapter sequence required to trim a sequence" />
328 <help> 325 <help>
329 326
330 **What it does** 327 **What it does**
331 328
332 TrimGalore!_ is a wrapper script that makes use of the publically available 329 TrimGalore!_ is a wrapper script that makes use of the publically available
333 adapter trimming tool Cutadapt and FastQC for optional quality control once 330 adapter trimming tool Cutadapt.
334 the trimming process has completed.
335 331
336 332
337 .. _TrimGalore!: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ 333 .. _TrimGalore!: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
338 334
339 335