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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <!--
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4 <package name="htslib" version="1.9"/>
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5 <package name="libbigwig" version="0.4.2"/>
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6 -->
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7 <package name="bamcount" version="0.4.0">
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8 <install version="1.0">
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9 <actions_group>
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10 <actions architecture="x86_64" os="linux">
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11 <action type="download_by_url">https://github.com/ChristopherWilks/bamcount/releases/download/0.4.0/bamcount-0.4.0_static.zip</action>
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12 <action type="move_directory_files">
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13 <source_directory>.</source_directory>
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14 <destination_directory>$INSTALL_DIR</destination_directory>
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15 </action>
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16 </actions>
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17 <action type="set_environment">
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18 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
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19 </action>
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20 </actions_group>
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21 </install>
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22 <readme><![CDATA[
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23 bamcount 0.4.0
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24
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25 BAM and BigWig utility.
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26
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27 Usage:
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28 bamcount <bam> [options]
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29
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30 Options:
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31 -h --help Show this screen.
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32 --version Show version.
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33 --threads # of threads to do BAM decompression
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34
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35 Extract basic junction information from the BAM, including co-occurrence
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36 --junctions <prefix> Extract jx coordinates, strand, and anchor length, per read
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37 Writes to a TSV file <prefix>.jxs.tsv
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38
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39 Extract reads from BAM into FASTQ (exclusive of all other modes):
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40 --bam2fastq <prefix> Extract all reads from the passed in BAM and output as FASTQs
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41 Uses prefix to name the fastq(s)
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42 --filter-out SAM bit flags to filter out
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43 --filter-in SAM bit flags to filter in
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44 --re-reverse If read is reversed in alignment, re-reverse it in output
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45 --one-file If you know file is not paired or just want all reads in one file
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46
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47 Non-reference summaries:
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48 --alts <prefix> Print differing from ref per-base coverages
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49 Writes to a CSV file <prefix>.alts.tsv
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50 --include-softclip <prefix> Print a record to the alts CSV for soft-clipped bases
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51 Writes total counts to a separate TSV file <prefix>.softclip.tsv
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52 --only-polya If --include-softclip, only print softclips which are mostly A's or T's
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53 --include-n Print mismatch records when mismatched read base is N
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54 --print-qual Print quality values for mismatched bases
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55 --delta Print POS field as +/- delta from previous
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56 --require-mdz Quit with error unless MD:Z field exists everywhere it's
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57 expected
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58 --no-head Don't print sequence names and lengths in header
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59
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60 Coverage and quantification:
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61 --coverage Print per-base coverage (slow but totally worth it)
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62 --auc <prefix> Print per-base area-under-coverage, will generate it for the genome
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63 and for the annotation if --annotation is also passed in
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64 Writes to a TSV file <prefix>.auc.tsv
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65 --bigwig <prefix> Output coverage as BigWig file(s). Writes to <prefix>.all.bw
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66 (also <prefix>.unique.bw when --min-unique-qual is specified).
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67 Requires libBigWig.
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68 --annotation <bed> <prefix>
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69 Path to BED file containing list of regions to sum coverage over
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70 (tab-delimited: chrm,start,end)
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71 --keep-bam-order Output annotation coverage in the order chromosomes appear in the BAM file.
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72 The default is to output annotation coverage in the order chromosomes appear in the BED file.
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73 --min-unique-qual <int>
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74 Output second bigWig consisting built only from alignments
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75 with at least this mapping quality. --bigwig must be specified.
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76 Also produces second set of annotation sums based on this coverage
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77 if --annotation is enabled
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78 --double-count Allow overlapping ends of PE read to count twice toward
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79 coverage
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80 --num-bases Report total sum of bases in alignments processed (that pass filters)
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81
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82 Other outputs:
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83 --read-ends Print counts of read starts/ends, if --min-unique-qual is set
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84 then only the alignments that pass that filter will be counted here
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85 Writes to 2 TSV files: <prefix>.starts.tsv, <prefix>.ends.tsv
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86 --frag-dist <prefix> Print fragment length distribution across the genome
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87 Writes to a TSV file <prefix>.frags.tsv
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88 --echo-sam Print a SAM record for each aligned read
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89 --ends Report end coordinate for each read (useful for debugging)
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90 --test-polya Lower Poly-A filter minimums for testing (only useful for debugging/testing)
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91 ]]></readme>
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92 </package>
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93 </tool_dependency>
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