<commit_before><macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="1.3.1">samtools</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@TOOL_VERSION@">1.3.1</token>
    <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token>
    <xml name="filter_options">
        <option value="1">Read is paired</option>
        <option value="2">Read is mapped in a proper pair</option>
        <option value="4">The read is unmapped</option>
        <option value="8">The mate is unmapped</option>
        <option value="16">Read strand</option>
        <option value="32">Mate strand</option>
        <option value="48">Read is the first in a pair</option>
        <option value="64">Read is the second in a pair</option>
        <option value="256">The alignment or this read is not primary</option>
        <option value="512">The read fails platform/vendor quality checks</option>
        <option value="768">The read is a PCR or optical duplicate</option>
        <option value="1024">Supplementary alignment</option>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @misc{SAM_def,
                title={Definition of SAM/BAM format},
                url = {https://samtools.github.io/hts-specs/},}
            </citation>
            <citation type="doi">10.1093/bioinformatics/btp352</citation>
            <citation type="doi">10.1093/bioinformatics/btr076</citation>
            <citation type="doi">10.1093/bioinformatics/btr509</citation>
            <citation type="bibtex">
                @misc{Danecek_et_al,
                Author={<NAME>., <NAME>., <NAME>.},
                title={Multiallelic calling model in bcftools (-m)},<commit_msg>samtools sort: missing changes to macros.xml<commit_after><macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="1.7">samtools</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@TOOL_VERSION@">1.7</token>
    <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token>
    <token name="@ADDTHREADS@">
        ##compute the number of ADDITIONAL threads to be used by samtools (-@)
        addthreads=\${GALAXY_SLOTS:-1} &amp;&amp; (( addthreads-- )) &amp;&amp;
    </token>
    <xml name="flag_options">
        <option value="1">read is paired</option>
        <option value="2">read is mapped in a proper pair</option>
        <option value="4">read is unmapped</option>
        <option value="8">mate is unmapped</option>
        <option value="16">read reverse strand</option>
        <option value="32">mate reverse strand</option>
        <option value="64">read is the first in a pair</option>
        <option value="128">read is the second in a pair</option>
        <option value="256">alignment or read is not primary</option>
        <option value="512">read fails platform/vendor quality checks</option>
        <option value="1024">read is a PCR or optical duplicate</option>
        <option value="2048">supplementary alignment</option>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @misc{SAM_def,
                title={Definition of SAM/BAM format},
                url = {https://samtools.github.io/hts-specs/},}
            </citation>
            <citation type="doi">10.1093/bioinformatics/btp352</citation>
            <citation type="doi">10.1093/bioinformatics/btr076</citation>
            <citation type="doi">10.1093/bioinformatics/btr509</citation>
            <citation type="bibtex">
                @misc{Danecek_et_al,
                Author={<NAME>., <NAME>., <NAME>.},
                title={Multiallelic calling model in bcftools (-m)},
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