# HG changeset patch # User iuc # Date 1485884547 18000 # Node ID d6e3d97e17f07c75964ff1f7661d198aee9e674d # Parent 98d4a7bfec8337bb0c9aff8990a8fd4c3a56f81b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e diff -r 98d4a7bfec83 -r d6e3d97e17f0 bcftools_convert_to_vcf.xml --- a/bcftools_convert_to_vcf.xml Mon Oct 03 12:15:07 2016 -0400 +++ b/bcftools_convert_to_vcf.xml Tue Jan 31 12:42:27 2017 -0500 @@ -12,16 +12,16 @@ #set $input_vcf = None #if $convert.convert_from == 'gvcf': #set $input_vcf = 'input.vcf.gz' - #if $convert.input_file.datatype.file_ext == 'vcf' + #if $convert.input_file.is_of_type('vcf') bgzip -c "$convert.input_file" > $input_vcf && bcftools index $input_vcf && - #elif $convert.input_file.datatype.file_ext == 'vcf_bgzip' + #elif $convert.input_file.is_of_type('vcf_bgzip') ln -s "$convert.input_file" $input_vcf - #elif $convert.input_file.datatype.file_ext == 'bcf' + #elif $convert.input_file.is_of_type('bcf') #set $input_vcf = 'input.bcf' - ln -s "$convert.input_file" $input_vcf && + ln -s "$convert.input_file" $input_vcf && bcftools index $input_vcf && - #elif $convert.input_file.datatype.file_ext == 'bcf_bgzip' + #elif $convert.input_file.is_of_type('bcf_bgzip') ln -s "$convert.input_file" $input_vcf && #end if #end if @@ -61,7 +61,7 @@ - diff -r 98d4a7bfec83 -r d6e3d97e17f0 macros.xml --- a/macros.xml Mon Oct 03 12:15:07 2016 -0400 +++ b/macros.xml Tue Jan 31 12:42:27 2017 -0500 @@ -14,14 +14,16 @@ bcftools htslib + samtools bcftools 2>&1 | grep 'Version:' - + 10.1093/bioinformatics/btp352 @@ -45,20 +47,20 @@ $input_vcf && bcftools index $input_vcf && -#elif $input_file.datatype.file_ext == 'vcf_bgzip' +#elif $input_file.is_of_type('vcf_bgzip') ln -s "$input_file" $input_vcf -#elif $input_file.datatype.file_ext == 'bcf' +#elif $input_file.is_of_type('bcf') #set $input_vcf = 'input.bcf' - ln -s "$input_file" $input_vcf && + ln -s "$input_file" $input_vcf && #if $input_file.metadata.bcf_index: ln -s $input_file.metadata.bcf_index ${input_vcf}.csi && - #else + #else bcftools index $input_vcf && #end if -#elif $input_file.datatype.file_ext == 'bcf_bgzip' +#elif $input_file.is_of_type('bcf_bgzip') ln -s "$input_file" $input_vcf #end if ]]> @@ -77,21 +79,21 @@ #set $vcfs_list_file = 'vcfs_list' #for (i,input_file) in enumerate($input_files): #set $input_vcf = 'input' + str($i) + '.vcf.gz' - #if $input_file.datatype.file_ext == 'vcf' + #if $input_file.is_of_type('vcf') bgzip -c "$input_file" > $input_vcf && bcftools index $input_vcf && - #elif $input_file.datatype.file_ext == 'vcf_bgz' + #elif $input_file.is_of_type('vcf_bgz') ln -s "$input_file" $input_vcf - #elif $input_file.datatype.file_ext == 'bcf' + #elif $input_file.is_of_type('bcf') #set $input_vcf = 'input' + str($i) + '.bcf.gz' ## bgzip -c "$input_file" > $input_vcf && ln -s "$input_file" $input_vcf && #if $input_file.metadata.bcf_index: ln -s $input_file.metadata.bcf_index ${input_vcf}.csi && - #else + #else bcftools index $input_vcf && #end if - #elif $input_file.datatype.file_ext == 'bcfvcf_bgz' + #elif $input_file.is_of_type('bcfvcf_bgz') ln -s "$input_file" $input_vcf && #end if echo '$input_vcf' >> $vcfs_list_file && @@ -225,7 +227,7 @@ - ^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$ @@ -272,7 +274,7 @@ - ^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$ @@ -299,7 +301,7 @@ $targets_path && @@ -331,7 +333,7 @@ - ^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$ @@ -358,15 +360,15 @@ - ^(\w+(,\w+)*)?$ - - - @@ -416,7 +418,7 @@ - ^([^,]+(,[^,]+)*)?$ @@ -443,7 +445,7 @@ Output Type ----------- -Output compressed BCF (b), or uncompressed VCF (v). +Output compressed BCF (b), or uncompressed VCF (v). Use the BCF option when piping between bcftools subcommands to speed up performance by removing unecessary compression/decompression and VCF<->BCF conversion.