| Previous changeset 14:4f7a47e3857c (2022-01-15) Next changeset 16:e075b1be5abb (2022-07-23) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612" |
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modified:
bcftools_annotate.xml |
| b |
| 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 @@ <?xml version='1.0' encoding='utf-8'?> -<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@"> +<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1"> <description>Annotate and edit VCF/BCF files</description> <macros> <token name="@EXECUTABLE@">annotate</token> @@ -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 '${section.remove}' #end if ## Default section @@ -118,8 +118,8 @@ Note that in case of tab-delimited file, the coordinates POS, FROM and TO are one-based and inclusive. ]]></help> </param> - <param name="header_file" type="data" format="txt" label="Header Lines File" optional="True" help="lines which should be appended to the VCF header" /> - <param name="header_lines" type="text" area="True" label="Header Lines" optional="True" help="lines which should be appended to the VCF header" > + <param name="header_file" type="data" format="txt" label="Header Lines File" optional="true" help="lines which should be appended to the VCF header" /> + <param name="header_lines" type="text" area="true" label="Header Lines" optional="true" help="lines which should be appended to the VCF header" > <help><![CDATA[ ##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description="Example header line"> ##INFO=<ID=STRING_TAG,Number=1,Type=String,Description="Yet another header line"> @@ -128,20 +128,20 @@ </param> </when> </conditional> - <param name="mark_sites" type="text" value="" label="Mark Sites TAG" + <param argument="--mark-sites" type="text" value="" label="Mark Sites TAG" help="add INFO/TAG flag to sites which are ("+") or are not ("-") listed in the annotations file" /> - <param name="set_id" type="text" value="" optional="true" label="Set Id"> + <param argument="--set-id" type="text" value="" optional="true" label="Set Id"> <help>Assign ID on the fly using the given format. By default all existing IDs are replaced. If the format string is preceded by "+", only missing IDs will be set. For example: '%CHROM\_%POS\_%REF\_%FIRST_ALT' </help> <sanitizer sanitize="False"/> - <validator type="regex" message="">^([+]?(%[A-Z]+)(\_%[A-Z]+)*)?$</validator> + <validator type="regex" message="">^([+]?(%[A-Z_]+)(\\_%[A-Z_]+)*)?$</validator> </param> </section> <section name="sec_annotate" expanded="false" title="Change Annotations"> - <param name="remove" type="text" value="" label="Remove annotations" optional="true"> + <param argument="--remove" type="text" value="" label="Remove annotations" optional="true"> <help><![CDATA[ List of annotations to remove. Use "FILTER" to remove all filters or "FILTER/SomeFilter" to remove a specific filter. @@ -151,7 +151,7 @@ ]]></help> <validator type="regex" message="">^(\^?[A-Z]+(/\w+)?(,\^?[A-Z]+(/\w+)?)*)?$</validator> </param> - <param name="rename_chrs" type="data" format="tabular" label="Rename CHROM" optional="True" + <param argument="--rename-chrs" type="data" format="tabular" label="Rename CHROM" optional="true" help="rename chromosomes according to the map in file, with old_name new_name pairs separated by whitespaces, each on a separate line." /> </section> <section name="sec_restrict" expanded="false" title="Restrict to"> @@ -182,14 +182,20 @@ </test> <test> <param name="input_file" ftype="vcf" value="annotate.vcf" /> - <param name="anno_fmt" value="tab" /> - <param name="annotations" value="annotate2.tab" /> - <param name="header_file" value="annotate.hdr" /> - <param name="columns" value="CHROM,FROM,TO,T_STR" /> + <section name="sec_annofile"> + <param name="columns" value="CHROM,FROM,TO,T_STR" /> + <conditional name="annofile"> + <param name="anno_fmt" value="tab" /> + <param name="annotations" value="annotate2.tab" /> + <param name="header_file" value="annotate.hdr" /> + </conditional> + <param name="set_id" value="%CHROM\_%POS\_%REF\_%FIRST_ALT" /> + </section> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> <has_text text="T_STR=region_3000150_3106154" /> + <has_text text="1_3062915_GTTT_G" /> </assert_contents> </output> </test> |