Mercurial > repos > weilong-guo > bs_seeker2

comparison BSseeker2/galaxy/bs_seeker2_wrapper.xml @ 1:8b26adf64adc draft default tip

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V2.0.5
author weilong-guo
date Tue, 05 Nov 2013 01:55:39 -0500
parents e6df770c0e58
children
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0:e6df770c0e58 1:8b26adf64adc
20 #end if 20 #end if
21 21
22 22
23 ### aligner 23 ### aligner
24 --align--aligner ${choosealigner.aligner} 24 --align--aligner ${choosealigner.aligner}
25 #if $choosealigner.aligner == "bowtie2"
26 #if $choosealigner.mode_type == "local"
27 --align--bt2--local
28 #else
29 --align--bt2--end-to-end
30 #end if
31 #end if
25 32
26 ### Index from history or built-in 33 ### Index from history or built-in
27 #if $choosealigner.rrbsFragments.refGenomeSource.genomeSource == "history" 34 #if $choosealigner.rrbsFragments.refGenomeSource.genomeSource == "history"
28 --build--file ${choosealigner.rrbsFragments.refGenomeSource.ownFile} 35 --build--file ${choosealigner.rrbsFragments.refGenomeSource.ownFile}
29 --build--aligner ${choosealigner.aligner} 36 --build--aligner ${choosealigner.aligner}
192 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> 199 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
193 </when> 200 </when>
194 </conditional> 201 </conditional>
195 </when> 202 </when>
196 </conditional> 203 </conditional>
204
205
206 <conditional name="mode_type">
207 <param name="mode" type="select" label="Select the mode of Bowtie2">
208 <option value="local" selected="true"> local alignment </option>
209 <option value="end_to_end" > end-to-end alignment </option>
210 </param>
211 </conditional>
197 </when> 212 </when>
198 </conditional> 213 </conditional>
199 <conditional name="adapterInfo"> 214 <conditional name="adapterInfo">
200 <param name="useAdapter" type="select" label="adapter sequence"> 215 <param name="useAdapter" type="select" label="adapter sequence">
201 <option value="noAdapter">No</option> 216 <option value="noAdapter">No</option>