|
0
|
1 <tool id="bamcount" name="Summarize coverage from a BAM (bamcount)" version="0.1.0">
|
|
|
2 <requirements>
|
|
|
3 <requirement type="package" version="0.2.6">bamcount</requirement>
|
|
|
4 </requirements>
|
|
|
5 <command detect_errors="exit_code"><![CDATA[
|
|
|
6 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
|
|
|
7 ]]></command>
|
|
|
8 <inputs>
|
|
|
9 <param type="data" name="input1" format="bam" />
|
|
|
10 </inputs>
|
|
|
11 <outputs>
|
|
|
12 <data name="output1" format="auc.tsv" from_work_dir="bc.auc.tsv" />
|
|
|
13 </outputs>
|
|
|
14 <tests>
|
|
|
15 <test>
|
|
|
16 <param name="input1" value="test.bam"/>
|
|
|
17 <output name="output1" file="bc.auc.tsv"/>
|
|
|
18 </test>
|
|
|
19 </tests>
|
|
|
20 <help><![CDATA[
|
|
|
21 bamcount 0.2.6
|
|
|
22
|
|
|
23 BAM and BigWig utility.
|
|
|
24
|
|
|
25 Usage:
|
|
|
26 bamcount <bam> [options]
|
|
|
27
|
|
|
28 Options:
|
|
|
29 -h --help Show this screen.
|
|
|
30 --version Show version.
|
|
|
31 --threads # of threads to do BAM decompression
|
|
|
32
|
|
|
33 Non-reference summaries:
|
|
|
34 --alts <prefix> Print differing from ref per-base coverages
|
|
|
35 Writes to a CSV file <prefix>.alts.tsv
|
|
|
36 --include-softclip Print a record for soft-clipped bases
|
|
|
37 --include-n Print mismatch records when mismatched read base is N
|
|
|
38 --print-qual Print quality values for mismatched bases
|
|
|
39 --delta Print POS field as +/- delta from previous
|
|
|
40 --require-mdz Quit with error unless MD:Z field exists everywhere it's
|
|
|
41 expected
|
|
|
42 --no-head Don't print sequence names and lengths in header
|
|
|
43
|
|
|
44 Coverage and quantification:
|
|
|
45 --coverage Print per-base coverage (slow but totally worth it)
|
|
|
46 --auc <prefix> Print per-base area-under-coverage, will generate it for the genome
|
|
|
47 and for the annotation if --annotation is also passed in
|
|
|
48 Writes to a TSV file <prefix>.auc.tsv
|
|
|
49 --bigwig <prefix> Output coverage as BigWig file(s). Writes to <prefix>.all.bw
|
|
|
50 (also <prefix>.unique.bw when --min-unique-qual is specified).
|
|
|
51 Requires libBigWig.
|
|
|
52 --annotation <bed> <prefix>
|
|
|
53 Path to BED file containing list of regions to sum coverage over
|
|
|
54 (tab-delimited: chrm,start,end)
|
|
|
55 --min-unique-qual <int>
|
|
|
56 Output second bigWig consisting built only from alignments
|
|
|
57 with at least this mapping quality. --bigwig must be specified.
|
|
|
58 Also produces second set of annotation sums based on this coverage
|
|
|
59 if --annotation is enabled
|
|
|
60 --double-count Allow overlapping ends of PE read to count twice toward
|
|
|
61 coverage
|
|
|
62 --num-bases Report total sum of bases in alignments processed (that pass filters)
|
|
|
63
|
|
|
64 Other outputs:
|
|
|
65 --read-ends Print counts of read starts/ends, if --min-unique-qual is set
|
|
|
66 then only the alignments that pass that filter will be counted here
|
|
|
67 Writes to 2 TSV files: <prefix>.starts.tsv, <prefix>.ends.tsv
|
|
|
68 --frag-dist <prefix> Print fragment length distribution across the genome
|
|
|
69 Writes to a TSV file <prefix>.frags.tsv
|
|
|
70 --echo-sam Print a SAM record for each aligned read
|
|
|
71 --ends Report end coordinate for each read (useful for debugging)
|
|
|
72 ]]></help>
|
|
|
73 <citations>
|
|
|
74 <citation type="bibtex">
|
|
|
75 @misc{githubbamcount,
|
|
|
76 author = {Wilks, Christopher},
|
|
|
77 year = {2019},
|
|
|
78 title = {bamcount},
|
|
|
79 publisher = {GitHub},
|
|
|
80 journal = {GitHub repository},
|
|
|
81 url = {https://github.com/BenLangmead/bamcount},
|
|
|
82 }</citation>
|
|
|
83 </citations>
|
|
|
84 </tool>
|
