# HG changeset patch # User iuc # Date 1646762339 0 # Node ID 2958e3b49ad41855dc282ac54d9fb1e745bdb35c # Parent 4f7a47e3857c0862d22a5ef7afecb657aaa98bc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612" diff -r 4f7a47e3857c -r 2958e3b49ad4 bcftools_annotate.xml --- a/bcftools_annotate.xml Sat Jan 15 13:40:18 2022 +0000 +++ b/bcftools_annotate.xml Tue Mar 08 17:58:59 2022 +0000 @@ -1,5 +1,5 @@ - + Annotate and edit VCF/BCF files annotate @@ -17,7 +17,7 @@ #if $section.annofile.anno_fmt == 'vcf': #if $section.annofile.annotations.is_of_type('vcf') #set $annotation_file = 'annotations.vcf.gz' - bgzip -c "$section.annofile.annotations" > $annotation_file && + bgzip -c '$section.annofile.annotations' > $annotation_file && bcftools index $annotation_file && #elif $section.annofile.annotations.is_of_type('bcf') #set $annotation_file = 'annotations.bcf' @@ -31,18 +31,18 @@ #elif $section.annofile.anno_fmt == 'tab': #if $section.annofile.annotations.is_of_type('bed') #set $annotation_file = 'annotations.bed.gz' - bgzip -c "$section.annofile.annotations" > $annotation_file && + bgzip -c '$section.annofile.annotations' > $annotation_file && tabix -s 1 -b 2 -e 3 $annotation_file && #else: #set $annotation_file = 'annotations.tab.gz' - bgzip -c "$section.annofile.annotations" > $annotation_file && + bgzip -c '$section.annofile.annotations' > $annotation_file && tabix -s 1 -b 2 -e 2 $annotation_file && #end if #if $section.annofile.header_file: #set $annotation_hdr = $section.annofile.header_file #elif $section.annofile.header_lines: #set $annotation_hdr = 'annotation.hdr' - grep '^\#\#INFO' ${hdr_file} > $annotation_hdr && + grep '^\#\#INFO' '${hdr_file}' > $annotation_hdr && #end if #end if #set $section = $sec_restrict @@ -53,25 +53,25 @@ #set $section = $sec_annofile @COLUMNS@ #if $annotation_file: - --annotations "${annotation_file}" + --annotations '${annotation_file}' #end if #if $annotation_hdr: - --header-lines "${annotation_hdr}" + --header-lines '${annotation_hdr}' #end if #if $section.set_id: - --set-id "${section.set_id}" + --set-id '${section.set_id}' #end if #if $section.mark_sites: - --mark-sites "${section.mark_sites}" + --mark-sites '${section.mark_sites}' #end if #set $section = $sec_annotate #if $section.rename_chrs: - --rename-chrs "${section.rename_chrs}" + --rename-chrs '${section.rename_chrs}' #end if #if $section.remove: - --remove "${section.remove}" + --remove '${section.remove}' #end if ## Default section @@ -118,8 +118,8 @@ Note that in case of tab-delimited file, the coordinates POS, FROM and TO are one-based and inclusive. ]]> - - + + ##INFO= @@ -128,20 +128,20 @@ - - + Assign ID on the fly using the given format. By default all existing IDs are replaced. If the format string is preceded by "+", only missing IDs will be set. For example: '%CHROM\_%POS\_%REF\_%FIRST_ALT' - ^([+]?(%[A-Z]+)(\_%[A-Z]+)*)?$ + ^([+]?(%[A-Z_]+)(\\_%[A-Z_]+)*)?$
- + ^(\^?[A-Z]+(/\w+)?(,\^?[A-Z]+(/\w+)?)*)?$ -
@@ -182,14 +182,20 @@ - - - - +
+ + + + + + + +
+