Mercurial > repos > weilong-guo > bs_seeker2
comparison BSseeker2/galaxy/bs_seeker2_wrapper.xml @ 1:8b26adf64adc draft default tip
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> |