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1 <tool id="sambamba_filter" name="Filter BAM or SAM" version="1.0">
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2 <requirements>
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3 <requirement type="package" version="0.3.3">sambamba</requirement>
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4 </requirements>
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5 <description>
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6 on flags, fields, and tags using Sambamba
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7 </description>
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8 <version_command>sambamba 2>&1 | grep "sambamba v" | sed 's/^sambamba v\(.*\)/\1/'</version_command>
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9 <command>
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10 #if $query != None:
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11 #set $query = $query.replace('__sq__', '\'')
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12 #set $query = $query.replace('__ob__', '[')
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13 #set $query = $query.replace('__cb__', ']')
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14 #set $query = $query.replace('__dq__', '"')
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15 #set $query = $query.replace('__oc__', '{')
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16 #set $query = $query.replace('__cc__', '}')
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17 #set $query = $query.replace('__gt__', chr(62))
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18 #set $query = $query.replace('__lt__', chr(60))
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19 #end if
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20 #set $input1 = 'input.bam'
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21 ln -s $input $input1 &&
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22 ln -s $input.metadata.bam_index input.bai &&
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23 sambamba view
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24 #if $query != "":
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25 --filter="$query"
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26 #end if
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27 -f bam -o $outfile $input1 $region
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28 </command>
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29 <inputs>
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30 <param name="input" type="data" format="bam" label="BAM or SAM file to filter"/>
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31 <param name="query" type="text" size="80">
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32 <label>Filter expression</label>
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33 <help>See below for query syntax.</help>
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34 </param>
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35
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36 <param name="region" type="text" size="40" label="Region in format chr:beg-end">
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37 <help>
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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.
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39 </help>
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40 </param>
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41 </inputs>
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42 <outputs>
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43 <data name="outfile" format="bam"></data>
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44 </outputs>
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45 <stdio>
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46 <exit_code range="1:" level="fatal" description="Error occured" />
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47 </stdio>
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48 <tests>
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49 <test>
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50 <param name="input" value="ex1_header.sam" ftype="sam" />
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51 <param name="query" value="[H0] == 1 and read_name =~ /^EAS51_62/" />
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52 <param name="format" value="bam" />
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53 <param name="region" value="" />
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54 <output name="outfile" file="ex1_header_filtered.bam" ftype="bam" />
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55 </test>
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56 <test>
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57 <param name="input" value="c1215_fixmate.bam" ftype="bam" />
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58 <param name="query" value="[MD] =~ /^\d+T\d+A\d+/ and first_of_pair" />
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59 <param name="format" value="sam" />
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60 <param name="region" value="AL096846:1000-5000" />
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61 <output name="outfile" file="c1215_fixmate_filtered.sam" ftype="sam" />
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62 </test>
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63 </tests>
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64 <help>
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65 Sambamba Filter Overview
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66 ========================
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67
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68 This tool uses the sambamba_ ``view`` command to filter BAM/SAM on flags, fields, tags, and region. Input is SAM or BAM file.
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69
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70
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71 Filter Syntax
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72 =============
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73
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74 Complete documentation of filter syntax is available at https://github.com/lomereiter/sambamba/wiki/%5Bsambamba-view%5D-Filter-expression-syntax.
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75
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76 A *filter expression* is a number of *basic conditions* linked by ``and``, ``or``, ``not`` logical operators, and enclosed in parentheses where needed.
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77
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78 *Basic condition* is a one for a single record field, tag, or flag.
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79
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80 You can use ``==,`` ``!=,`` ``>``, ``<``, ``>=``, ``<=`` comparison operators for both integers and strings.
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81
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82 Strings are delimited by single quotes, if you need a single quote inside a string, escape it with ``\\``.
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83
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84 Examples of filter expressions
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85 ------------------------------
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86
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87 ::
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88
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89 mapping_quality >= 30 and ([RG] =~ /^abcd/ or [NM] == 7)
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90 read_name == 'abc\'def'
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91
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92 Basic conditions for flags
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93 --------------------------
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94
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95 The following flag names are recognized:
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96 * paired
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97 * proper_pair
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98 * unmapped
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99 * mate_is_unmapped
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100 * reverse_strand
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101 * mate_is_reverse_strand
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102 * first_of_pair
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103 * second_of_pair
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104 * secondary_alignment
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105 * failed_quality_control
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106 * duplicate
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107
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108 Example
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109 ~~~~~~~
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110
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111 ::
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112
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113 not (unmapped or mate_is_unmapped) and first_of_pair
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114
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115 Basic conditions for fields
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116 ---------------------------
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117
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118 Conditions for integer and string fields are supported.
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119
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120 List of integer fields:
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121 * ref_id
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122 * position
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123 * mapping_quality
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124 * sequence_length
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125 * mate_ref_id
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126 * mate_position
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127 * template_length
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128
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129
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130 List of string fields:
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131 * read_name
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132 * sequence
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133 * cigar
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134
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135
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136 Example
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137 ~~~~~~~
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138
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139 ::
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140
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141 ref_id == 3 and mapping_quality >= 50 and sequence_length >= 80
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142
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143 Basic conditions for tags
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144 -------------------------
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145
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146 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.
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147
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148 In order to do filtering based on the presence of a particular tag, you can use special ``null`` value.
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149
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150 Example
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151 ~~~~~~~
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152
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153 ::
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154
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155 [RG] != null and [AM] == 37
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156
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157 -----
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158
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159 .. _sambamba: http://github.com/lomereiter/sambamba
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160 .. _filter-syntax: https://github.com/lomereiter/sambamba/wiki/%5Bsambamba-view%5D-Filter-expression-syntax
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161
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162 </help>
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163 </tool>
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