<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Create intersections, unions and complements of VCF files</description>
    <macros>
        <token name="@EXECUTABLE@">isec</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="aggressive"><![CDATA[
@PREPARE_INPUT_FILES@
#set $section = $sec_restrict
@PREPARE_TARGETS_FILE@
@PREPARE_REGIONS_FILE@

bcftools @EXECUTABLE@

## Default section
#set $section = $sec_default
${section.complement}
#if $section.nfiles:
  --nfiles "${section.nfiles}"
#end if

#set $section = $sec_restrict
@REGIONS@
@TARGETS@
@COLLAPSE@
@APPLY_FILTERS@
@INCLUDE@
@EXCLUDE@

@OUTPUT_TYPE@
@THREADS@

## Primary Input/Outputs
@INPUT_FILES@
> '$output_file'

]]>
    </command>
    <inputs>
        <expand macro="macro_inputs"/>
        <section name="sec_restrict" expanded="false" title="Restrict to">
            <expand macro="macro_collapse"/>
            <expand macro="macro_include"/>
            <expand macro="macro_exclude"/>
            <expand macro="macro_apply_filters"/>
            <expand macro="macro_region_restrict"/>
            <expand macro="macro_target_restrict"/>
        </section>
        <section name="sec_default" expanded="true" title="Isec Options">
            <param argument="--nfiles" type="text" label="Nfiles" help="Output positions present in this many (=), this many or more (+), this many or fewer (-), the exact (~) files">
                <validator type="regex" message="bitmask zero or one">^([=+-]?\d+|~[01]+)?$</validator>
            </param>
            <param name="complement" type="boolean" truevalue="--complement" falsevalue="" label="Complement" help="Output positions present only in the first file but missing in the others"/>
            <!-- <param name="prefix" type="boolean" truevalue="\-\-prefix subset" falsevalue="" checked="false" label="subset each of the input files"  
                   help="(-p)" />-->
            <!-- <param name="write" type="text" label="Files to write" optional="True" 
                 help="(-write) The output files to write " >
                <validator type="regex" message="">^([=+-]?\d+|~[01]+)?$</validator>
            </param>-->
        </section>
        <expand macro="macro_select_output_type"/>
    </inputs>
    <outputs>
        <expand macro="macro_vcf_output"/>
    </outputs>
    <tests>
        <test>
            <param name="input_files" ftype="vcf" value="isec.b.vcf,isec.a.vcf"/>
            <section name="sec_default">
                <param name="nfiles" value="=2"/>
            </section>
            <param name="output_type" value="v"/>
            <output name="output_file">
                <assert_contents>
                    <has_text text="3157410"/>
                    <has_text text="3162006"/>
                    <not_has_text text="3062915"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test region overlap option -->
        <test>
            <param name="input_files" ftype="vcf" value="isec.b.vcf,isec.a.vcf"/>
            <section name="sec_default">
                <param name="nfiles" value="=2"/>
            </section>
            <param name="output_type" value="v"/>
            <section name="sec_restrict">
                <conditional name="regions">
                    <param name="regions_src" value="regions" />
                    <repeat name="region_specs">
                        <param name="chrom" value="1" />
                    </repeat>
                </conditional>
            </section>
            <output name="output_file">
                <assert_contents>
                    <has_text text="3157410"/>
                    <has_text text="3162006"/>
                    <not_has_text text="3062915"/>
                </assert_contents>
            </output>
            <assert_command>
                <has_text text="--regions-overlap"/>
            </assert_command>
        </test>
    </tests>
    <help><![CDATA[
=====================================
 bcftools @EXECUTABLE@
=====================================

Create intersections, unions and complements of VCF files.

@COLLAPSE_HELP@
@REGIONS_HELP@
@TARGETS_HELP@
@EXPRESSIONS_HELP@

@BCFTOOLS_MANPAGE@#@EXECUTABLE@

@BCFTOOLS_HOWTOS@
]]>
    </help>
    <expand macro="citations"/>
</tool>