Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
comparison samtools-parallel-mpileup.xml @ 42:bf9c5a61b200
overwrite readonly files
| author | yhoogstrate <y.hoogstrate@erasmusmc.nl> |
|---|---|
| date | Wed, 05 Mar 2014 13:34:36 +0100 |
| parents | 48c78adade03 |
| children | c800d09b8cc3 |
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| 41:b4185ce77360 | 42:bf9c5a61b200 |
|---|---|
| 180 <data format="mpileup" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" /> | 180 <data format="mpileup" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" /> |
| 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" dbkey="hg19" /> | 185 <param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" /> |
| 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="extended_parameters_regions.samtools_regions" value="entire_genome" /> |
| 188 | 188 |
| 189 <param name="mpileup_parallelization.mpileup_parallelization_select" value="false" /> | 189 <param name="mpileup_parallelization.mpileup_parallelization_select" value="false" /> |
| 190 <param name="sort_mpileup" value="true" /> | 190 <param name="sort_mpileup" value="true" /> |
| 193 | 193 |
| 194 | 194 |
| 195 <output name="output" file="hg19_mutant.mpileup" /> | 195 <output name="output" file="hg19_mutant.mpileup" /> |
| 196 </test> | 196 </test> |
| 197 <test><!-- Use parallelized samtools --> | 197 <test><!-- Use parallelized samtools --> |
| 198 <param name="alignments" value="hg19_mutant.bam" dbkey="hg19" /> | 198 <param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" /> |
| 199 <param name="reference_genome_source.source_select" value="attribute" /> | 199 <param name="reference_genome_source.source_select" value="attribute" /> |
| 200 <param name="extended_parameters_regions.samtools_regions" value="entire_genome" /> | 200 <param name="extended_parameters_regions.samtools_regions" value="entire_genome" /> |
| 201 | 201 |
| 202 <param name="mpileup_parallelization.mpileup_parallelization_select" value="true" /> | 202 <param name="mpileup_parallelization.mpileup_parallelization_select" value="true" /> |
| 203 <param name="mpileup_parallelization.samtools_threads" value="2" /> | 203 <param name="mpileup_parallelization.samtools_threads" value="2" /> |