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1 <tool id="bamcount" name="Summarize coverage from a BAM (bamcount)" version="0.2.0">
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2 <requirements>
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3 <requirement type="package" version="0.4.0">bamcount</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 bamcount "$input1" --threads $threads --coverage --no-head --min-unique-qual $min_uniq_qual --frag-dist bc --bigwig bc --auc bc --alts bc --junctions bc
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7 ]]></command>
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8 <inputs>
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9 <param type="integer" name="threads" value="1" />
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10 <param type="integer" name="min_uniq_qual" value="10" />
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11 <param type="file" name="input1" format="bam" />
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12 <param type="file" name="annotation" format="bed" />
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13 </inputs>
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14 <outputs>
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15 <data name="output1" format="txt" from_work_dir="bc.auc.tsv" />
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16 <data name="output2" format="txt" from_work_dir="bc.alts.tsv" />
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17 <data name="output3" format="txt" from_work_dir="bc.frags.tsv" />
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18 <data name="output4" format="txt" from_work_dir="bc.jxs.tsv" />
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19 <!--
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20 <data name="output5" format="bed" from_work_dir="bc.all.tsv" />
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21 <data name="output6" format="bed" from_work_dir="bc.unique.tsv" />
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22 -->
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23 <data name="output7" format="bigwig" from_work_dir="bc.all.bw" />
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24 <data name="output8" format="bigwig" from_work_dir="bc.unique.bw" />
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="input1" value="test.bam"/>
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29 <output name="output1" file="test.auc.tsv"/>
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30 </test>
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31 </tests>
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32 <help><![CDATA[
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33 bamcount 0.4.0
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34
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35 BAM and BigWig utility.
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36
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37 Usage:
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38 bamcount <bam> [options]
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39
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40 Options:
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41 -h --help Show this screen.
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42 --version Show version.
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43 --threads # of threads to do BAM decompression
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44
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45 Extract basic junction information from the BAM, including co-occurrence
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46 --junctions <prefix> Extract jx coordinates, strand, and anchor length, per read
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47 Writes to a TSV file <prefix>.jxs.tsv
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48
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49 Extract reads from BAM into FASTQ (exclusive of all other modes):
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50 --bam2fastq <prefix> Extract all reads from the passed in BAM and output as FASTQs
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51 Uses prefix to name the fastq(s)
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52 --filter-out SAM bit flags to filter out
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53 --filter-in SAM bit flags to filter in
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54 --re-reverse If read is reversed in alignment, re-reverse it in output
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55 --one-file If you know file is not paired or just want all reads in one file
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56
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57 Non-reference summaries:
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58 --alts <prefix> Print differing from ref per-base coverages
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59 Writes to a CSV file <prefix>.alts.tsv
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60 --include-softclip <prefix> Print a record to the alts CSV for soft-clipped bases
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61 Writes total counts to a separate TSV file <prefix>.softclip.tsv
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62 --only-polya If --include-softclip, only print softclips which are mostly A's or T's
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63 --include-n Print mismatch records when mismatched read base is N
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64 --print-qual Print quality values for mismatched bases
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65 --delta Print POS field as +/- delta from previous
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66 --require-mdz Quit with error unless MD:Z field exists everywhere it's
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67 expected
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68 --no-head Don't print sequence names and lengths in header
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69
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70 Coverage and quantification:
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71 --coverage Print per-base coverage (slow but totally worth it)
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72 --auc <prefix> Print per-base area-under-coverage, will generate it for the genome
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73 and for the annotation if --annotation is also passed in
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74 Writes to a TSV file <prefix>.auc.tsv
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75 --bigwig <prefix> Output coverage as BigWig file(s). Writes to <prefix>.all.bw
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76 (also <prefix>.unique.bw when --min-unique-qual is specified).
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77 Requires libBigWig.
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78 --annotation <bed> <prefix>
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79 Path to BED file containing list of regions to sum coverage over
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80 (tab-delimited: chrm,start,end)
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81 --keep-bam-order Output annotation coverage in the order chromosomes appear in the BAM file.
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82 The default is to output annotation coverage in the order chromosomes appear in the BED file.
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83 --min-unique-qual <int>
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84 Output second bigWig consisting built only from alignments
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85 with at least this mapping quality. --bigwig must be specified.
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86 Also produces second set of annotation sums based on this coverage
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87 if --annotation is enabled
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88 --double-count Allow overlapping ends of PE read to count twice toward
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89 coverage
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90 --num-bases Report total sum of bases in alignments processed (that pass filters)
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91
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92 Other outputs:
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93 --read-ends Print counts of read starts/ends, if --min-unique-qual is set
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94 then only the alignments that pass that filter will be counted here
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95 Writes to 2 TSV files: <prefix>.starts.tsv, <prefix>.ends.tsv
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96 --frag-dist <prefix> Print fragment length distribution across the genome
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97 Writes to a TSV file <prefix>.frags.tsv
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98 --echo-sam Print a SAM record for each aligned read
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99 --ends Report end coordinate for each read (useful for debugging)
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100 --test-polya Lower Poly-A filter minimums for testing (only useful for debugging/testing)
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101 ]]></help>
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102 <citations>
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103 <citation type="bibtex">
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104 @misc{githubbamcount,
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105 author = {Wilks, Christopher},
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106 year = {2019},
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107 title = {bamcount},
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108 publisher = {GitHub},
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109 journal = {GitHub repository},
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110 url = {https://github.com/ChristopherWilks/bamcount},
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111 }</citation>
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112 </citations>
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113 </tool>
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