Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
comparison samtools-parallel-mpileup.xml @ 52:b2dc8ab51a79 draft
Uploaded
| author | yhoogstrate |
|---|---|
| date | Wed, 05 Mar 2014 09:18:21 -0500 |
| parents | 11292b6c3c6c |
| children | 3296b5c8a968 |
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| 51:11292b6c3c6c | 52:b2dc8ab51a79 |
|---|---|
| 181 </outputs> | 181 </outputs> |
| 182 | 182 |
| 183 <tests> | 183 <tests> |
| 184 <test><!-- Use classical samtools --> | 184 <test><!-- Use classical samtools --> |
| 185 <param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" ftype="bam" /> | 185 <param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" ftype="bam" /> |
| 186 <param name="reference_genome_source.source_select" value="attribute" /> | 186 <!-- <param name="reference_genome_source.source_select" value="attribute" /> --> |
| 187 <param name="extended_parameters_regions.samtools_regions" value="entire_genome" /> | 187 <param name="source_select" value="attribute" /> |
| 188 | 188 <!-- <param name="extended_parameters_regions.samtools_regions" value="entire_genome" /> --> |
| 189 <param name="mpileup_parallelization.mpileup_parallelization_select" value="false" /> | 189 <param name="samtools_regions" value="entire_genome" /> |
| 190 | |
| 191 <!-- <param name="mpileup_parallelization.mpileup_parallelization_select" value="false" /> --> | |
| 192 <param name="mpileup_parallelization_select" value="false" /> | |
| 190 <param name="sort_mpileup" value="true" /> | 193 <param name="sort_mpileup" value="true" /> |
| 191 | 194 |
| 192 <param name="extended_parameters.parameters" value="default" /> | 195 <!-- <param name="extended_parameters.parameters" value="default" /> --> |
| 196 <param name="parameters" value="default" /> | |
| 193 | 197 |
| 194 | 198 |
| 195 <output name="output" file="hg19_mutant.mpileup" /> | 199 <output name="output" file="hg19_mutant.mpileup" /> |
| 196 </test> | 200 </test> |
| 197 <test><!-- Use parallelized samtools --> | 201 <test><!-- Use parallelized samtools --> |
| 198 <param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" ftype="bam" /> | 202 <param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" ftype="bam" /> |
| 199 <param name="reference_genome_source.source_select" value="attribute" /> | 203 <!-- <param name="reference_genome_source.source_select" value="attribute" /> --> |
| 200 <param name="extended_parameters_regions.samtools_regions" value="entire_genome" /> | 204 <param name="source_select" value="attribute" /> |
| 201 | 205 <!-- <param name="extended_parameters_regions.samtools_regions" value="entire_genome" /> --> |
| 202 <param name="mpileup_parallelization.mpileup_parallelization_select" value="true" /> | 206 <param name="samtools_regions" value="entire_genome" /> |
| 203 <param name="mpileup_parallelization.samtools_threads" value="2" /> | 207 |
| 208 <!-- <param name="mpileup_parallelization.mpileup_parallelization_select" value="true" /> --> | |
| 209 <param name="mpileup_parallelization_select" value="true" /> | |
| 210 <!-- <param name="mpileup_parallelization.samtools_threads" value="2" /> --> | |
| 211 <param name="samtools_threads" value="2" /> | |
| 204 <param name="sort_mpileup" value="true" /> | 212 <param name="sort_mpileup" value="true" /> |
| 205 | 213 |
| 206 <param name="extended_parameters.parameters" value="default" /> | 214 <!-- <param name="extended_parameters.parameters" value="default" /> --> |
| 215 <param name="parameters" value="default" /> | |
| 207 | 216 |
| 208 | 217 |
| 209 <output name="output" file="hg19_mutant.mpileup" /> | 218 <output name="output" file="hg19_mutant.mpileup" /> |
| 210 </test> | 219 </test> |
| 211 </tests> | 220 </tests> |