<tool id="bcftools_reheader" name="BCFtools reheader" version="1.0.0">
    <description>Modify header of VCF/BCF files, change sample names</description>
    <command>
        #if str( $input_file_index ) != "None":
            ln -s -f $input input_file.${input.ext} &amp;&amp;
            ln -s -f $input_file_index input_file.${input.ext}.tbi &amp;&amp;
        #end if

        bcftools reheader
        --output "${output_file}"
        #if str( $header ) != "None":
            --header "${header}"
        #end if
        #if str( $samples ) != "None":
            --samples "${samples}"
        #end if
        #if str( $input_file_index ) != "None":
            input_file.${input.ext}
        #else
            $input
        #end if
    </command>
    <inputs>
        <param name="input" type="data" format="vcf,bcf,bgzip" label="VCF or BCF input file" help="Input file can optionally be compressed and indexed using Bgzip and Tabix Galaxy tools. In this case, select bgzipped file here and index below."/>
        <param name="input_file_index" type="data" optional="true" label="Input file index" help="Tabix-generated index for input file. Run Tabix Galaxy tool on bgzipped input file to create index."/>
        <param name="header" type="data" optional="True" label="New VCF header" help="-h"/>
        <param name="samples" type="data" optional="True" label="New sample names" help="-s. Either new sample names, each on a separate line, in the same order as samples appear in the VCF file, or &quot;old_name new_name\n&quot; pairs separated by whitespaces, each on a separate line." />
    </inputs>
    <outputs>
        <data name="output_file" format_source="input" label="${tool.name} on ${on_string}" />
    </outputs>
    <help>
**About this tool**

**BCFtools reheader**: Modify header of VCF/BCF files, change sample names.

Please see https://samtools.github.io/bcftools/bcftools.html for more info on options.
  </help>
</tool>