<tool id="bcftools_filter" name="BCFtools filter" version="1.0.0">
    <description>Apply fixed-threshold filters</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 filter                    
        --output "${output_file}"
        --output-type "${output_type}"
        #if str( $regions_file ) != "None":
            --regions-file "${regions_file}"
        #end if
        #if str( $regions ) != "":
            --regions "${regions}"
        #end if
        #if str( $targets_file ) != "None":
            --targets-file "${targets_file}"
        #end if
        #if str( $targets ) != "":
            --targets "${targets}"
        #end if
        #if str( $expr_cond.set_expr ) == "True":
            #if str( $expr_cond.include_or_exclude ) == "include":
                --include "${expr_cond.expr}"
            #else
                --exclude "${expr_cond.expr}"
            #end if
        #end if
        #if str( $mode_plus ) == "true":
            #if str( $mode_x ) == "true":
                --mode +x
            #else
                --mode +
            #end if
        #elif str( $mode_x ) == "true"
            --mode x
        #end if
        #if str( $soft_filter_cond.set_soft_filter ) == "True":
            #if str( $soft_filter_cond.string_or_plus_cond.string_or_plus ) == "use_plus":
                --soft-filter +
            #else
                --soft-filter "${soft_filter_cond.string_or_plus_cond.str}"
            #end if
        #end if
        #if str( $set_gts_cond.set_gts ) == "True":
            #if str( $set_gts_cond.gts ) == "period":
                --set-GTs .
            #else
                --set-GTs 0
            #end if
        #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="output_type" type="select" label="Output data type">
            <option value="v" selected="true">VCF</option>
            <option value="b">BCF</option>
        </param>
        <param name="regions_file" type="data" optional="true" label="Regions file" help="-R. Regions specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/>
        <param name="regions" type="text" size="80" optional="True" label="Regions list" help="-r. Comma-separated list of regions. Format: chr|chr:pos|chr:from-to|chr:from-[,...]">
            <sanitizer invalid_char="">
                <valid initial="string.digits"><add value="CHRchr-:,"/> </valid>
            </sanitizer>
        </param>
        <param name="targets_file" type="data" optional="true" label="Targets file" help="-T. Targets specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/>
        <param name="targets" type="text" size="80" optional="True" label="Targets list" help="-t. Comma-separated list of targets. Format: [^]chr|chr:pos|chr:from-to|chr:from-[,...]">
            <sanitizer invalid_char="">
                <valid initial="string.digits"><add value="CHRchr-:,^"/> </valid>
            </sanitizer>
        </param>
        <conditional name="expr_cond">
            <param name="set_expr" type="boolean" checked="False" label="Filter by expression" help="-i, e. Include/ exclude sites for which expression is true. Must use valid expression."/>
            <when value="true">
                <param name="include_or_exclude" type="select" label="Include or exclude by expression">
                    <option value="include">Include</option>
                    <option value="exclude">Exclude</option>
                </param>
                <param name="expr" type="text" size="80" label="Expression">
                    <sanitizer invalid_char="">
                        <valid initial="string.letters,string.digits"><add value="~`!@#$%^&amp;*()-_=+[{]}\|;:'&quot;,&lt;.&gt;?/ " /> </valid>
                    </sanitizer>
                </param>
            </when>
        </conditional>
        <param name="mode_x" type="boolean" checked="False" label="For sites that pass filter, reset filter to &quot;PASS&quot;" help="-m x. Default: When FILTER string is empty, set filter to &quot;PASS&quot;. Do not change FILTER string otherwise."/>
        <param name="mode_plus" type="boolean" checked="False" label="For sites that fail filter, append new FILTER string to existing FILTER string" help="-m +. Default: Replace existing FILTER string with new FILTER string."/>
        <conditional name="soft_filter_cond">
            <param name="set_soft_filter" type="boolean" checked="False" label="Annotate FILTER column" help="-s"/>
            <when value="true">
                <conditional name="string_or_plus_cond">
                    <param name="string_or_plus" type="select" label="Annotation string">
                        <option value="use_plus" selected="true">Annotate with a pre-generated unique string  (&quot;Filter1&quot;, &quot;Filter2&quot;, etc.)</option>
                        <option value="use_str">Choose annotation string</option>
                    </param>
                    <when value="use_str">
                        <param name="str" type="text" size="80" label="String to annotate with" />
                    </when>
                </conditional>
            </when>
        </conditional>
        <conditional name="set_gts_cond">
            <param name="set_gts" type="boolean" checked="False" label="Set genotype of samples that fail filter" help="-S"/>
            <when value="true">
                <param name="gts" type="select" label="Genotype of failed samples">
                    <option value="period" selected="true">.</option>
                    <option value="ref_allele">Reference allele</option>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_file" format="vcf" label="${tool.name} on ${on_string}">
            <change_format>
                <when input="output_type" value="b" format="bcf" />
            </change_format>
        </data>
    </outputs>
    <help>
**About this tool**

**BCFtools filter**: Apply fixed-threshold filters.

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