Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 52:b2dc8ab51a79 draft
Uploaded
| author | yhoogstrate |
|---|---|
| date | Wed, 05 Mar 2014 09:18:21 -0500 |
| parents | 11292b6c3c6c |
| children | 77578b1e98e4 |
| files | samtools-parallel-mpileup.xml varscan_mpileup2snp.xml varscan_mpileup2snp_from_bam.xml |
| diffstat | 3 files changed, 40 insertions(+), 19 deletions(-) [+] |
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--- a/samtools-parallel-mpileup.xml Wed Mar 05 08:47:37 2014 -0500 +++ b/samtools-parallel-mpileup.xml Wed Mar 05 09:18:21 2014 -0500 @@ -183,27 +183,36 @@ <tests> <test><!-- Use classical samtools --> <param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" ftype="bam" /> - <param name="reference_genome_source.source_select" value="attribute" /> - <param name="extended_parameters_regions.samtools_regions" value="entire_genome" /> + <!-- <param name="reference_genome_source.source_select" value="attribute" /> --> + <param name="source_select" value="attribute" /> + <!-- <param name="extended_parameters_regions.samtools_regions" value="entire_genome" /> --> + <param name="samtools_regions" value="entire_genome" /> - <param name="mpileup_parallelization.mpileup_parallelization_select" value="false" /> + <!-- <param name="mpileup_parallelization.mpileup_parallelization_select" value="false" /> --> + <param name="mpileup_parallelization_select" value="false" /> <param name="sort_mpileup" value="true" /> - <param name="extended_parameters.parameters" value="default" /> + <!-- <param name="extended_parameters.parameters" value="default" /> --> + <param name="parameters" value="default" /> <output name="output" file="hg19_mutant.mpileup" /> </test> <test><!-- Use parallelized samtools --> <param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" ftype="bam" /> - <param name="reference_genome_source.source_select" value="attribute" /> - <param name="extended_parameters_regions.samtools_regions" value="entire_genome" /> + <!-- <param name="reference_genome_source.source_select" value="attribute" /> --> + <param name="source_select" value="attribute" /> + <!-- <param name="extended_parameters_regions.samtools_regions" value="entire_genome" /> --> + <param name="samtools_regions" value="entire_genome" /> - <param name="mpileup_parallelization.mpileup_parallelization_select" value="true" /> - <param name="mpileup_parallelization.samtools_threads" value="2" /> + <!-- <param name="mpileup_parallelization.mpileup_parallelization_select" value="true" /> --> + <param name="mpileup_parallelization_select" value="true" /> + <!-- <param name="mpileup_parallelization.samtools_threads" value="2" /> --> + <param name="samtools_threads" value="2" /> <param name="sort_mpileup" value="true" /> - <param name="extended_parameters.parameters" value="default" /> + <!-- <param name="extended_parameters.parameters" value="default" /> --> + <param name="parameters" value="default" /> <output name="output" file="hg19_mutant.mpileup" />
--- a/varscan_mpileup2snp.xml Wed Mar 05 08:47:37 2014 -0500 +++ b/varscan_mpileup2snp.xml Wed Mar 05 09:18:21 2014 -0500 @@ -63,7 +63,10 @@ <tests> <test> <param name="mpileup_input" value="hg19_mutant.mpileup" dbkey="hg19" ftype="bam" /> - <param name="extended_parameters.parameters" value="default" /> + + <!-- <param name="extended_parameters.parameters" value="default" /> --> + <param name="parameters" value="default" /> + <param name="varscan_output_vcf" value="1" /> <output name="snv_output" file="hg19_mutant.vcf" />
--- a/varscan_mpileup2snp_from_bam.xml Wed Mar 05 08:47:37 2014 -0500 +++ b/varscan_mpileup2snp_from_bam.xml Wed Mar 05 09:18:21 2014 -0500 @@ -226,13 +226,17 @@ <tests> <test><!-- Use classical samtools --> <param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" ftype="bam" /> - <param name="reference_genome_source.source_select" value="attribute" /> - <param name="extended_parameters_regions.samtools_regions" value="entire_genome" /> + <!-- <param name="reference_genome_source.source_select" value="attribute" /> --> + <param name="source_select" value="attribute" /> + <!-- <param name="extended_parameters_regions.samtools_regions" value="entire_genome" /> --> + <param name="samtools_regions" value="entire_genome" /> - <param name="mpileup_parallelization.mpileup_parallelization_select" value="false" /> + <!-- <param name="mpileup_parallelization.mpileup_parallelization_select" value="false" /> --> + <param name="mpileup_parallelization_select" value="false" /> <param name="sort_mpileup" value="true" /> - <param name="extended_parameters.parameters" value="default" /> + <!-- <param name="extended_parameters.parameters" value="default" /> --> + <param name="parameters" value="default" /> <param name="varscan_output_vcf" value="1" /> @@ -240,14 +244,19 @@ </test> <test><!-- Use parallelized samtools --> <param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" ftype="bam" /> - <param name="reference_genome_source.source_select" value="attribute" /> - <param name="extended_parameters_regions.samtools_regions" value="entire_genome" /> + <!-- <param name="reference_genome_source.source_select" value="attribute" /> --> + <param name="source_select" value="attribute" /> + <!-- <param name="extended_parameters_regions.samtools_regions" value="entire_genome" /> --> + <param name="samtools_regions" value="entire_genome" /> - <param name="mpileup_parallelization.mpileup_parallelization_select" value="true" /> - <param name="mpileup_parallelization.samtools_threads" value="2" /> + <!-- <param name="mpileup_parallelization.mpileup_parallelization_select" value="true" /> --> + <param name="mpileup_parallelization_select" value="true" /> + <!-- <param name="mpileup_parallelization.samtools_threads" value="2" /> --> + <param name="samtools_threads" value="2" /> <param name="sort_mpileup" value="true" /> - <param name="extended_parameters.parameters" value="default" /> + <!-- <param name="extended_parameters.parameters" value="default" /> --> + <param name="parameters" value="default" /> <param name="varscan_output_vcf" value="1" />