<tool id="samtools_fixmate" name="Samtools fixmate" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>fill mate coordinates, ISIZE and mate related flags</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
        @ADDTHREADS@
        ## name sort input
        #if not $bamfile.is_of_type('qname_sorted.bam', 'qnamed_input_sorted.bam'):
            samtools sort
            -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
            -n
            -O BAM
            -o namesorted.bam
            '$bamfile' &&
        #else:
            ln -s '$bamfile' namesorted.bam &&
        #end if

        samtools fixmate
            -@ \$addthreads
            $remsec
            $noprop
            $tempcigar
            $addms
            -O BAM
            namesorted.bam
            '$output'
    ]]></command>
    <inputs>
        <param name="bamfile" type="data" format="sam,bam,cram" optional="false" label="Select alignment" help="Set of aligned reads." />
        <param name="remsec" type="boolean" argument="-r" truevalue="-r" falsevalue="" checked="false" label="Remove secondary and unmapped reads" />
        <param name="noprop" type="boolean" argument="-p" truevalue="-p" falsevalue="" checked="false" label="Disable FR proper pair check" />
        <param name="tempcigar" type="boolean" argument="-c" truevalue="-c" falsevalue="" checked="false" label="Add template cigar ct tag" />
        <param name="addms" type="boolean" argument="-m" truevalue="-m" falsevalue="" checked="false" label="Add ms (mate score) tags" help="These are used by markdup to select the best reads to keep." />
    </inputs>
    <outputs>
	   <!--<data name="output" format="sam" />-->
	   <data name="output" format="qname_sorted.bam"/>
    </outputs>
    <tests>
        <!-- from https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2493-->
        <!--    test_cmd($opts,out=>'fixmate/1_coord_sort.sam.expected', err=>'fixmate/1_coord_sort.sam.expected.err', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/1_coord_sort.sam -", expect_fail=>1);-->
        <test>
            <param name="bamfile" value="2_isize_overflow.sam" ftype="sam" />
            <output name="output" file="2_isize_overflow.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
        </test>
        <!--    test_cmd($opts,out=>'fixmate/2_isize_overflow.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/2_isize_overflow.sam -");-->
        <test>
            <param name="bamfile" value="3_reverse_read_pp_lt.sam" ftype="sam" />
            <output name="output" file="3_reverse_read_pp_lt.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
        </test>
        <!--    test_cmd($opts,out=>'fixmate/3_reverse_read_pp_lt.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/3_reverse_read_pp_lt.sam -");-->
        <test>
            <param name="bamfile" value="4_reverse_read_pp_equal.sam" ftype="sam" />
            <output name="output" file="4_reverse_read_pp_equal.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
        </test>
        <!--    test_cmd($opts,out=>'fixmate/4_reverse_read_pp_equal.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/4_reverse_read_pp_equal.sam -");-->
        <test>
            <param name="bamfile" value="5_ct.sam" ftype="sam" />
            <param name="tempcigar" value="-c" />
            <output name="output" file="5_ct.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
        </test>
        <!--    test_cmd($opts,out=>'fixmate/5_ct.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/5_ct.sam -");-->
        <test>
            <param name="bamfile" value="6_ct_replace.sam" ftype="sam" />
            <param name="tempcigar" value="-c" />
            <output name="output" file="6_ct_replace.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
        </test>
        <!--    test_cmd($opts,out=>'fixmate/6_ct_replace.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/6_ct_replace.sam -");-->
        <test>
            <param name="bamfile" value="7_two_read_mapped.sam" ftype="sam" />
            <output name="output" file="7_two_read_mapped.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
        </test>
        <!--test_cmd($opts,out=>'fixmate/7_two_read_mapped.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/7_two_read_mapped.sam -");-->
    </tests>
    <help>
**What it does**

Fill in mate coordinates, ISIZE and mate related flags from a name-sorted alignment.
    </help>
    <expand macro="citations"/>
</tool>