view bamcount.xml @ 0:1f0e3aaaba19 draft

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<tool id="bamcount" name="Summarize coverage from a BAM (bamcount)" version="0.1.0">
    <requirements>
        <requirement type="package" version="0.2.6">bamcount</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        bamcount "$input1" --threads $threads --coverage --no-head --require-mdz --min-unique-qual $min_uniq_qual --frag-dist bc --bigwig bc --annotation $annotation bc --auc bc --alts bc
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="bam" />
    </inputs>
    <outputs>
        <data name="output1" format="auc.tsv" from_work_dir="bc.auc.tsv" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="test.bam"/>
            <output name="output1" file="bc.auc.tsv"/>
        </test>
    </tests>
    <help><![CDATA[
        bamcount 0.2.6

    BAM and BigWig utility.

    Usage:
      bamcount <bam> [options]

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

    Non-reference summaries:
      --alts <prefix>      Print differing from ref per-base coverages
                           Writes to a CSV file <prefix>.alts.tsv
      --include-softclip   Print a record for soft-clipped bases
      --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)
      --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)
    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubbamcount,
  author = {Wilks, Christopher},
  year = {2019},
  title = {bamcount},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/BenLangmead/bamcount},
}</citation>
    </citations>
</tool>