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<?xml version="1.0"?>
<tool_dependency>
<!--
    <package name="htslib" version="1.9"/>
    <package name="libbigwig" version="0.4.2"/>
-->
    <package name="bamcount" version="0.4.0">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="linux">
                    <action type="download_by_url">https://github.com/ChristopherWilks/bamcount/releases/download/0.4.0/bamcount</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme><![CDATA[
bamcount 0.4.0

BAM and BigWig utility.

Usage:
  bamcount <bam> [options]

Options:
  -h --help            Show this screen.
  --version            Show version.
  --threads            # of threads to do BAM decompression

Extract basic junction information from the BAM, including co-occurrence
  --junctions <prefix> Extract jx coordinates, strand, and anchor length, per read
                       Writes to a TSV file <prefix>.jxs.tsv

Extract reads from BAM into FASTQ (exclusive of all other modes):
  --bam2fastq <prefix> Extract all reads from the passed in BAM and output as FASTQs
                       Uses prefix to name the fastq(s)
  --filter-out         SAM bit flags to filter out
  --filter-in          SAM bit flags to filter in
  --re-reverse         If read is reversed in alignment, re-reverse it in output
  --one-file           If you know file is not paired or just want all reads in one file

Non-reference summaries:
  --alts <prefix>              Print differing from ref per-base coverages
                               Writes to a CSV file <prefix>.alts.tsv
  --include-softclip <prefix>  Print a record to the alts CSV for soft-clipped bases
                               Writes total counts to a separate TSV file <prefix>.softclip.tsv
  --only-polya                 If --include-softclip, only print softclips which are mostly A's or T's
  --include-n                  Print mismatch records when mismatched read base is N
  --print-qual                 Print quality values for mismatched bases
  --delta                      Print POS field as +/- delta from previous
  --require-mdz                Quit with error unless MD:Z field exists everywhere it's
                               expected
  --no-head                    Don't print sequence names and lengths in header

Coverage and quantification:
  --coverage           Print per-base coverage (slow but totally worth it)
  --auc <prefix>       Print per-base area-under-coverage, will generate it for the genome
                       and for the annotation if --annotation is also passed in
                       Writes to a TSV file <prefix>.auc.tsv
  --bigwig <prefix>    Output coverage as BigWig file(s).  Writes to <prefix>.all.bw
                       (also <prefix>.unique.bw when --min-unique-qual is specified).
                       Requires libBigWig.
  --annotation <bed> <prefix>
                       Path to BED file containing list of regions to sum coverage over
                       (tab-delimited: chrm,start,end)
  --keep-bam-order     Output annotation coverage in the order chromosomes appear in the BAM file.
                       The default is to output annotation coverage in the order chromosomes appear in the BED file.
  --min-unique-qual <int>
                       Output second bigWig consisting built only from alignments
                       with at least this mapping quality.  --bigwig must be specified.
                       Also produces second set of annotation sums based on this coverage
                       if --annotation is enabled
  --double-count       Allow overlapping ends of PE read to count twice toward
                       coverage
  --num-bases          Report total sum of bases in alignments processed (that pass filters)

Other outputs:
  --read-ends          Print counts of read starts/ends, if --min-unique-qual is set
                       then only the alignments that pass that filter will be counted here
                       Writes to 2 TSV files: <prefix>.starts.tsv, <prefix>.ends.tsv
  --frag-dist <prefix> Print fragment length distribution across the genome
                       Writes to a TSV file <prefix>.frags.tsv
  --echo-sam           Print a SAM record for each aligned read
  --ends               Report end coordinate for each read (useful for debugging)
  --test-polya         Lower Poly-A filter minimums for testing (only useful for debugging/testing)
]]></readme>
    </package>
</tool_dependency>