<?xml version="1.0"?>
<tool_dependency>
    <package name="bcftools" version="1.2">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="linux">
                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/bcftools/bcftools-1.2-Linux-x86_64.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <actions>
                    <action type="download_by_url">https://github.com/samtools/bcftools/releases/download/1.2/bcftools-1.2.tar.bz2</action>
                    <action type="shell_command">sed -i.bak 's#/usr/local#$INSTALL_DIR#' Makefile</action>
                    <action type="shell_command">make</action>
                    <action type="shell_command">make install</action>
                </actions>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="set_to" name="BCFTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme>
<![CDATA[
Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)
Version: 1.2 (using htslib 1.2.1)

Usage:   bcftools <command> <argument>

Commands:

 -- Indexing
    index        index VCF/BCF files

 -- VCF/BCF manipulation
    annotate     annotate and edit VCF/BCF files
    concat       concatenate VCF/BCF files from the same set of samples
    convert      convert VCF/BCF files to different formats and back
    isec         intersections of VCF/BCF files
    merge        merge VCF/BCF files files from non-overlapping sample sets
    norm         left-align and normalize indels
    plugin       user-defined plugins
    query        transform VCF/BCF into user-defined formats
    reheader     modify VCF/BCF header, change sample names
    view         VCF/BCF conversion, view, subset and filter VCF/BCF files

 -- VCF/BCF analysis
    call         SNP/indel calling
    consensus    create consensus sequence by applying VCF variants
    filter       filter VCF/BCF files using fixed thresholds
    gtcheck      check sample concordance, detect sample swaps and contamination
    roh          identify runs of autozygosity (HMM)
    stats        produce VCF/BCF stats

 Most commands accept VCF, bgzipped VCF, and BCF with the file type detected
 automatically even when streaming from a pipe. Indexed VCF and BCF will work
 in all situations. Un-indexed VCF and BCF and streams will work in most but
 not all situations.
]]>
        </readme>
    </package>
</tool_dependency>
Add tool dependency for bcftools 1.2
Add tool dependency for bcftools 1.2
