Mercurial > repos > devteam > freebayes
changeset 7:d0997bd93c49 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
| author | iuc |
|---|---|
| date | Thu, 04 May 2017 11:34:00 -0400 |
| parents | 3aacf7637e02 |
| children | b0ff6447545f |
| files | freebayes.xml |
| diffstat | 1 files changed, 20 insertions(+), 15 deletions(-) [+] |
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--- a/freebayes.xml Wed Feb 08 12:40:47 2017 -0500 +++ b/freebayes.xml Thu May 04 11:34:00 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-2"> +<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-3"> <description>bayesian genetic variant detector</description> <macros> <import>macros.xml</import> @@ -35,14 +35,25 @@ ln -s -f '${Tabixized_input}' 'input_variant_vcf.vcf.gz.tbi' && #end if - #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ): - samtools view -H b_${bam_count}.bam | - grep "^@SQ" | - cut -f 2- | - awk '{ gsub("^SN:","",$1); - gsub("^LN:","",$2); - print $1"\t0\t"$2; }' >> regions_all.bed && - #end for + ##if user has specified a region or target file, just use instead of calculating a set of unique regions + + #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file": + ln -s '${target_limit_type.input_target_bed}' regions_all.bed && + #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region": + printf '${target_limit_type.region_chromosome}\t${target_limit_type.region_start}\t${target_limit_type.region_end}' > regions_all.bed && + #else + ##divide up the regions in the bam file for efficient processing + #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ): + samtools view -H b_${bam_count}.bam | + grep "^@SQ" | + cut -f 2- | + awk '{ gsub("^SN:","",$1); + gsub("^LN:","",$2); + print $1"\t0\t"$2; }' >> regions_all.bed && + #end for + #end if + + sort -u regions_all.bed > regions_uniq.bed && ## split into even small chunks, this has some disatvantages and will not be used for the moment @@ -73,12 +84,6 @@ ## Outputs --vcf './vcf_output/part_\$i.vcf' - #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file": - --targets '${target_limit_type.input_target_bed}' - #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region": - --region '${target_limit_type.region_chromosome}:${target_limit_type.region_start}..${target_limit_type.region_end}' - #end if - ##advanced options #if str( $options_type.options_type_selector ) == "simple": ##do nothing as command like build up to this point is sufficinet for simple diploid calling