Mercurial > repos > lomereiter > sambamba_filter
annotate sambamba_filter.xml @ 5:123168c85390
updated to 0.4.7; use precompiled binaries
| author | lomereiter <lomereiter@gmail.com> |
|---|---|
| date | Tue, 04 Nov 2014 18:34:37 +0300 |
| parents | a03e95059256 |
| children |
| rev | line source |
|---|---|
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123168c85390
updated to 0.4.7; use precompiled binaries
lomereiter <lomereiter@gmail.com>
parents:
3
diff
changeset
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1 <tool id="sambamba_filter" name="Filter BAM or SAM" version="1.1"> |
| 3 | 2 <requirements> |
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5
123168c85390
updated to 0.4.7; use precompiled binaries
lomereiter <lomereiter@gmail.com>
parents:
3
diff
changeset
|
3 <requirement type="package" version="0.4.7">sambamba</requirement> |
| 3 | 4 </requirements> |
| 5 <description> | |
| 6 on flags, fields, and tags using Sambamba | |
| 7 </description> | |
| 8 <version_command>sambamba 2>&1 | grep "sambamba v" | sed 's/^sambamba v\(.*\)/\1/'</version_command> | |
| 9 <command> | |
| 10 #if $query != None: | |
| 11 #set $query = $query.replace('__sq__', '\'') | |
| 12 #set $query = $query.replace('__ob__', '[') | |
| 13 #set $query = $query.replace('__cb__', ']') | |
| 14 #set $query = $query.replace('__dq__', '"') | |
| 15 #set $query = $query.replace('__oc__', '{') | |
| 16 #set $query = $query.replace('__cc__', '}') | |
| 17 #set $query = $query.replace('__gt__', chr(62)) | |
| 18 #set $query = $query.replace('__lt__', chr(60)) | |
| 19 #end if | |
| 20 #set $input1 = 'input.bam' | |
| 21 ln -s $input $input1 && | |
| 22 ln -s $input.metadata.bam_index input.bai && | |
|
5
123168c85390
updated to 0.4.7; use precompiled binaries
lomereiter <lomereiter@gmail.com>
parents:
3
diff
changeset
|
23 sambamba view -t \${GALAXY_SLOTS:-8} |
| 3 | 24 #if $query != "": |
| 25 --filter="$query" | |
| 26 #end if | |
| 27 -f bam -o $outfile $input1 $region | |
| 28 </command> | |
| 29 <inputs> | |
| 30 <param name="input" type="data" format="bam" label="BAM or SAM file to filter"/> | |
| 31 <param name="query" type="text" size="80"> | |
| 32 <label>Filter expression</label> | |
| 33 <help>See below for query syntax.</help> | |
| 34 </param> | |
| 35 | |
| 36 <param name="region" type="text" size="40" label="Region in format chr:beg-end"> | |
| 37 <help> | |
| 38 Regions can be specified as 'chr2' (the whole chr2), 'chr2:1000000' (region starting from 1,000,000bp) or 'chr2:1,000,000-2,000,000' (region between 1,000,000 and 2,000,000bp including the end points). The coordinates are 1-based. | |
| 39 </help> | |
| 40 </param> | |
| 41 </inputs> | |
| 42 <outputs> | |
| 43 <data name="outfile" format="bam"></data> | |
| 44 </outputs> | |
| 45 <stdio> | |
| 46 <exit_code range="1:" level="fatal" description="Error occured" /> | |
| 47 </stdio> | |
| 48 <tests> | |
| 49 <test> | |
| 50 <param name="input" value="ex1_header.sam" ftype="sam" /> | |
| 51 <param name="query" value="[H0] == 1 and read_name =~ /^EAS51_62/" /> | |
| 52 <param name="format" value="bam" /> | |
| 53 <param name="region" value="" /> | |
| 54 <output name="outfile" file="ex1_header_filtered.bam" ftype="bam" /> | |
| 55 </test> | |
| 56 <test> | |
| 57 <param name="input" value="c1215_fixmate.bam" ftype="bam" /> | |
| 58 <param name="query" value="[MD] =~ /^\d+T\d+A\d+/ and first_of_pair" /> | |
| 59 <param name="format" value="sam" /> | |
| 60 <param name="region" value="AL096846:1000-5000" /> | |
| 61 <output name="outfile" file="c1215_fixmate_filtered.sam" ftype="sam" /> | |
| 62 </test> | |
| 63 </tests> | |
| 64 <help> | |
| 65 Sambamba Filter Overview | |
| 66 ======================== | |
| 67 | |
| 68 This tool uses the sambamba_ ``view`` command to filter BAM/SAM on flags, fields, tags, and region. Input is SAM or BAM file. | |
| 69 | |
| 70 | |
| 71 Filter Syntax | |
| 72 ============= | |
| 73 | |
| 74 A *filter expression* is a number of *basic conditions* linked by ``and``, ``or``, ``not`` logical operators, and enclosed in parentheses where needed. | |
| 75 | |
| 76 *Basic condition* is a one for a single record field, tag, or flag. | |
| 77 | |
| 78 You can use ``==,`` ``!=,`` ``>``, ``<``, ``>=``, ``<=`` comparison operators for both integers and strings. | |
| 79 | |
| 80 Strings are delimited by single quotes, if you need a single quote inside a string, escape it with ``\\``. | |
| 81 | |
| 82 Examples of filter expressions | |
| 83 ------------------------------ | |
| 84 | |
| 85 :: | |
| 86 | |
| 87 mapping_quality >= 30 and ([RG] =~ /^abcd/ or [NM] == 7) | |
| 88 read_name == 'abc\'def' | |
| 89 | |
| 90 Basic conditions for flags | |
| 91 -------------------------- | |
| 92 | |
| 93 The following flag names are recognized: | |
| 94 * paired | |
| 95 * proper_pair | |
| 96 * unmapped | |
| 97 * mate_is_unmapped | |
| 98 * reverse_strand | |
| 99 * mate_is_reverse_strand | |
| 100 * first_of_pair | |
| 101 * second_of_pair | |
| 102 * secondary_alignment | |
| 103 * failed_quality_control | |
| 104 * duplicate | |
| 105 | |
| 106 Example | |
| 107 ~~~~~~~ | |
| 108 | |
| 109 :: | |
| 110 | |
| 111 not (unmapped or mate_is_unmapped) and first_of_pair | |
| 112 | |
| 113 Basic conditions for fields | |
| 114 --------------------------- | |
| 115 | |
| 116 Conditions for integer and string fields are supported. | |
| 117 | |
| 118 List of integer fields: | |
| 119 * ref_id | |
| 120 * position | |
| 121 * mapping_quality | |
| 122 * sequence_length | |
| 123 * mate_ref_id | |
| 124 * mate_position | |
| 125 * template_length | |
| 126 | |
| 127 | |
| 128 List of string fields: | |
| 129 * read_name | |
| 130 * sequence | |
| 131 * cigar | |
| 132 | |
| 133 | |
| 134 Example | |
| 135 ~~~~~~~ | |
| 136 | |
| 137 :: | |
| 138 | |
| 139 ref_id == 3 and mapping_quality >= 50 and sequence_length >= 80 | |
| 140 | |
| 141 Basic conditions for tags | |
| 142 ------------------------- | |
| 143 | |
| 144 Tags are denoted by their names in square brackets, for instance, ``[RG]`` or ``[Q2].`` They support conditions for both integers and strings, i.e. the tag must also hold value of the corresponding type. | |
| 145 | |
| 146 In order to do filtering based on the presence of a particular tag, you can use special ``null`` value. | |
| 147 | |
| 148 Example | |
| 149 ~~~~~~~ | |
| 150 | |
| 151 :: | |
| 152 | |
| 153 [RG] != null and [AM] == 37 | |
| 154 | |
| 155 ----- | |
| 156 | |
| 157 .. _sambamba: http://github.com/lomereiter/sambamba | |
| 158 | |
| 159 </help> | |
| 160 </tool> |