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comparison trim_galore_wrapper.xml @ 1:c6de70bc43ee draft default tip

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Small fix for rrbs data.
author bjoern-gruening
date Sun, 24 Mar 2013 15:08:46 -0400
parents 2fd029916856
children
comparison
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0:2fd029916856 1:c6de70bc43ee
1 <tool id="trim_galore" name="Trim Galore" version="0.2.4.0"> 1 <tool id="trim_galore" name="Trim Galore" version="0.2.4.1">
2 <!-- Wrapper compatible with Trim Galore version 0.2.4.0 --> 2 <!-- Wrapper compatible with Trim Galore version 0.2.4.0 -->
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>
47 ## RBBS specific options. 47 ## RBBS specific options.
48 ## 48 ##
49 49
50 #if $rrbs.settingsType == "custom": 50 #if $rrbs.settingsType == "custom":
51 51
52 $rrbs 52 $rrbs.rrbs
53 $non_directional 53 $rrbs.non_directional
54 54
55 #end if 55 #end if
56 56
57 ## 57 ##
58 ## Creating a temporary directory where trim_galore will store all result files 58 ## Creating a temporary directory where trim_galore will store all result files
202 <param name="length_2" type="integer" value="35" label="Unpaired single-end read length cutoff needed for read 2 to be written" /> 202 <param name="length_2" type="integer" value="35" label="Unpaired single-end read length cutoff needed for read 2 to be written" />
203 </when> <!-- output --> 203 </when> <!-- output -->
204 </conditional> <!-- retain_unpaired --> 204 </conditional> <!-- retain_unpaired -->
205 205
206 </when> <!-- full --> 206 </when> <!-- full -->
207 </conditional> <!-- params --> 207 </conditional> <!-- params -->
208 208
209 <conditional name="rrbs"> 209 <conditional name="rrbs">
210 <param name="settingsType" type="select" label="RRBS specific settings"> 210 <param name="settingsType" type="select" label="RRBS specific settings">
211 <option value="default">Use Defaults</option> 211 <option value="default">Use Defaults (no RRBS)</option>
212 <option value="custom">Full parameter list</option> 212 <option value="custom">Full parameter list</option>
213 </param> 213 </param>
214 <when value="default" /> 214 <when value="default" />
215 <!-- Full/advanced params. --> 215 <!-- Full/advanced params. -->
216 <when value="custom"> 216 <when value="custom">