comparison bcftools_annotate.xml @ 9:a80ec64f9101 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653

8:2f09d9744e0b

<?xml version='1.0' encoding='utf-8'?>
<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>
        <import>macros.xml</import>
    </macros>

@PREPARE_INPUT_FILE@
#set $annotation_file = None
#set $annotation_hdr = None
#set $section = $sec_annofile
#if $section.annofile.anno_fmt == 'vcf':
  #set $annotation_file = 'annotations.vcf.gz'
  bgzip -c "$section.annofile.annotations" > $annotation_file &&
  bcftools index $annotation_file &&
#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 &&
    tabix -s 1 -b 2 -e 3 $annotation_file &&

                    <option value="vcf">From a VCF/BCF file</option>
                    <option value="tab">From a BED or tab-delimited file</option>
                </param>
                <when value="none"/>
                <when value="vcf">
                    <param name="annotations" type="data" format="vcf" label="Annotations VCF"/>
                </when>
                <when value="tab">
                    <param name="annotations" type="data" format="tabular,bed" label="Annotations">
                        <help><![CDATA[
                        BED, or a tab-delimited file with mandatory columns CHROM, POS (or, alternatively, FROM and TO),

                    <has_text text="STR=testSNP" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_file" ftype="vcf" value="annotate2.vcf" />
            <param name="anno_fmt" value="vcf" />
            <param name="annotations" value="annots2.vcf" />
            <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" />
            <param name="output_type" value="v" />

9:a80ec64f9101

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy2">
    <description>Annotate and edit VCF/BCF files</description>
    <macros>
        <token name="@EXECUTABLE@">annotate</token>
        <import>macros.xml</import>
    </macros>

@PREPARE_INPUT_FILE@
#set $annotation_file = None
#set $annotation_hdr = None
#set $section = $sec_annofile
#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 &&
    bcftools index $annotation_file &&
  #elif $section.annofile.annotations.is_of_type('bcf')
    #set $annotation_file = 'annotations.bcf'
    ln -s '$section.annofile.annotations' $annotation_file &&
    #if $section.annofile.annotations.metadata.bcf_index:
      ln -s '${section.annofile.annotations.metadata.bcf_index}' ${annotation_file}.csi &&
    #else
      bcftools index $annotation_file &&
    #end if
  #end if
#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 &&
    tabix -s 1 -b 2 -e 3 $annotation_file &&

                    <option value="vcf">From a VCF/BCF file</option>
                    <option value="tab">From a BED or tab-delimited file</option>
                </param>
                <when value="none"/>
                <when value="vcf">
                    <param name="annotations" type="data" format="vcf,bcf" label="Annotations VCF"/>
                </when>
                <when value="tab">
                    <param name="annotations" type="data" format="tabular,bed" label="Annotations">
                        <help><![CDATA[
                        BED, or a tab-delimited file with mandatory columns CHROM, POS (or, alternatively, FROM and TO),

                    <has_text text="STR=testSNP" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_file" ftype="vcf" value="annotate.vcf" />
            <param name="anno_fmt" value="vcf" />
            <param name="annotations" value="annots.bcf" />
            <param name="columns" value="STR,ID,QUAL,FILTER" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="idIndel" />
                    <has_text text="STR=testSNP" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_file" ftype="vcf" value="annotate2.vcf" />
            <param name="anno_fmt" value="vcf" />
            <param name="annotations" value="annots2.vcf" />
            <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" />
            <param name="output_type" value="v" />