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1 <tool id="bamFilter" name="bamFilter" version="0.0.1">
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2 <description>Filter BAM files on a variety of attributes</description>
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3 <requirements>
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4 <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement>
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5 </requirements>
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6 <command>
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7
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8 cat $script_file > $out_file2;
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9
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10 #for $bam_count, $input_bam in enumerate( $input_bams ):
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11 ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &&
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12 ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&
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13 #end for
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14
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15 bamtools
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16 filter
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17 -script $script_file
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18
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19 #for $bam_count, $input_bam in enumerate( $input_bams ):
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20 -in "localbam_${bam_count}.bam"
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21 #end for
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22 -out $out_file1
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23
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24 </command>
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25
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26 <inputs>
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27 <repeat name="input_bams" title="BAM dataset(s) to filter" min="1">
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28 <param name="input_bam" type="data" format="bam" label="BAM dataset" />
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29 </repeat>
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30 <repeat name="conditions" title="Condition" min="1">
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31 <repeat name="filters" title="Filter" min="1">
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32 <conditional name="bam_property">
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33 <param name="bam_property_selector" type="select" label="Select BAM property to filter on">
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34 <option value="alignmentFlag"/>
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35 <option value="cigar"/>
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36 <option value="insertSize"/>
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37 <option value="isDuplicate"/>
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38 <option value="isFailedQC"/>
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39 <option value="isFirstMate"/>
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40 <option value="isMapped"/>
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41 <option value="isMateMapped"/>
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42 <option value="isMateReverseStrand"/>
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43 <option value="isPaired"/>
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44 <option value="isPrimaryAlignment"/>
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45 <option value="isProperPair"/>
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46 <option value="isReverseStrand"/>
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47 <option value="isSecondMate"/>
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48 <option selected="True" value="mapQuality"/>
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49 <option value="matePosition"/>
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50 <option value="mateReference"/>
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51 <option value="name"/>
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52 <option value="position"/>
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53 <option value="queryBases"/>
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54 <option value="reference"/>
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55 <option value="tag"/>
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56 </param>
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57 <!-- would be fanstastic to have AND and OR constructs in when statements -->
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58 <when value="alignmentFlag">
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59 <param name="bam_property_value" type="integer" value="3" label="Filter on this alignment flag" help="Default (3) is for a paired read mapped in a proper pair"/>
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60 </when>
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61 <when value="cigar">
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62 <param name="bam_property_value" type="text" size="10" value="101M" label="Filter on this CIGAR string" help="Default (101M) is for 101 continuously matched bases"/>
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63 </when>
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64 <when value="insertSize">
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65 <param name="bam_property_value" type="text" size="10" value=">=250" label="Filter on inster size" help="You can use >, <, =, and ! (not) in your expression. E.g., to select pairs with inster size above 250 nt use ">=250"">
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66 <sanitizer invalid_char="">
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67 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid>
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68 </sanitizer>
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69 </param>
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70 </when>
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71 <when value="isDuplicate">
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72 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads makwed as duplicates" help="Checked = Read IS Duplicate, Empty = Read is NOT Duplicate" />
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73 </when>
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74 <when value="isFailedQC">
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75 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads failing QC" help="Checked = Failed QC, Empty = Passed QC"/>
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76 </when>
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77 <when value="isFirstMate">
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78 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select first mate in a read pair" help="Checked = is first mate, Empty = is NOT first mate"/>
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79 </when>
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80 <when value="isMapped">
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81 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Selected mapped reads" help="Checked = Mapped, Empty = NOT mapped"/>
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82 </when>
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83 <when value="isMateMapped">
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84 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads with mapped mate" help="Checked = Mate IS mapped Empty = Mate is NOT mapped"/>
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85 </when>
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86 <when value="isMateReverseStrand">
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87 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads with mate on the reverse strand" help="Checked = Mate IS on reverse strand, Empty = Mate is NOT on the reverse strand"/>
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88 </when>
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89 <when value="isPaired">
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90 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select paired reads" help="Checked = Read IS paired, Empty = Read is NOT paired"/>
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91 </when>
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92 <when value="isPrimaryAlignment">
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93 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select BAM records for primary alignments" help="Checked = Alignment IS primary, Empty = Alignment is NOT primary"/>
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94 </when>
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95 <when value="isProperPair">
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96 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select properly paired reads" help="Checked = Read IS in proper pair, Empty = Read is NOT in the proper pair"/>
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97 </when>
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98 <when value="isReverseStrand">
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99 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads in the reverse strand only" help="Checked = Read IS on the reverse strand, Empty = Read is NOT on the reverse strand"/>
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100 </when>
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101 <when value="isSecondMate">
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102 <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select second mate in a read pair" help="Checked = Read IS second mate, Empty = Read is NOT second mate"/>
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103 </when>
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104 <when value="mapQuality">
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105 <param name="bam_property_value" type="text" value="20" label="Filter on read mapping quality (phred scale)" help="You can use >, <, =, and ! (not) in your expression. E.g., to select reads with mapping quality of at least 30 use ">=30"">
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106 <sanitizer invalid_char="">
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107 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid>
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108 </sanitizer>
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109 </param>
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110 </when>
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111 <when value="matePosition">
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112 <param name="bam_property_value" type="text" value="1000000" label="Filter on the position of the mate" help="You can use >, <, =, and ! (not) in your expression. E.g., to select reads with mate (second end) mapping after position 1,000,000 use ">1000000"">
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113 <sanitizer invalid_char="">
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114 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid>
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115 </sanitizer>
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116 </param>
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117 </when>
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118 <when value="mateReference">
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119 <param name="bam_property_value" type="text" value="chr22" label="Filter on reference name for the mate" help="You can use = and ! (not) in your expression. E.g., to select reads with mates mapping to chrM use "chr22"">
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120 <sanitizer invalid_char="">
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121 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid>
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122 </sanitizer>
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123 </param>
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124 </when>
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125 <when value="name">
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126 <param name="bam_property_value" type="text" label="Filter on read name" help="You can use = and ! (not) in your expression.">
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127 <sanitizer invalid_char="">
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128 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid>
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129 </sanitizer>
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130 </param>
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131 </when>
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132 <when value="position">
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133 <param name="bam_property_value" type="text" value="500000" label="Filter on the position of the read" help="You can use >, <, =, and ! (not) in your expression. E.g., to select reads mapping after position 5,000 use ">5000"">
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134 <sanitizer invalid_char="">
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135 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid>
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136 </sanitizer>
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137 </param>
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138 </when>
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139 <when value="queryBases">
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140 <param name="bam_property_value" type="text" value="ttagggttagg" label="Filter on a sequence motif" help="You can use ! (not) in your expression">
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141 <sanitizer invalid_char="">
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142 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid>
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143 </sanitizer>
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144 </param>
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145 </when>
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146 <when value="reference">
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147 <param name="bam_property_value" type="text" value="chr22" label="Filter on the reference name for the read" help="You can use ! (not) in your expression">
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148 <sanitizer invalid_char="">
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149 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid>
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150 </sanitizer>
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151 </param>
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152 </when>
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153 <when value="tag">
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154 <param name="bam_property_value" type="text" value="NM:>1" label="Filter on a particular tag" help="You can use >, <, =, and ! (not).
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155 Tag name and its value must be separated by ":". E.g., to obtain reads with at least one mismatch use "NM:>1"">
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156 <sanitizer invalid_char="">
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157 <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value=":!="/></valid>
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158 </sanitizer>
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159 </param>
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160 </when>
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161 </conditional>
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162 </repeat>
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163 </repeat>
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164 <conditional name="rule_configuration">
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165 <param name="rules_selector" type="boolean" truevalue="true" falsevalue="false" label="Would you like to set rules?" help="Allows complex logical constructs. See Example 4 below." />
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166 <when value="true">
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167 <param name="rules" type="text" size="20" label="Enter rules here" help="This option can only be used with at least two conditions. Read help below (Example 4) to understand how it works." >
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168 <sanitizer invalid_char="">
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169 <valid initial="string.printable"/>
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170 </sanitizer>
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171 </param>
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172 </when>
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173 </conditional>
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174 </inputs>
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175
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176 <configfiles>
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177 <configfile name="script_file">
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178 ##Sets up a json configfile for bamtools filter
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179 ##If there is more than one condition prints brackets and "filters:"
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180 #if len( $conditions ) > 1
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181 {
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182 "filters":
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183 [
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184 #end if
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185 #for $i, $c in enumerate( $conditions, start=1 )
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186 { "id": "$i",
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187 #for $j, $s in enumerate( $c.filters, start=1 )
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188 ##The if below takes care of the comma at the end of last condition within group
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189 #if $j != len( $c.filters)
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190 "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}",
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191 #else
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192 "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}"
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193 #end if
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194 #end for
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195 ##The if below takes care of the comma at the end of last condition within group
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196 #if $i != len( $conditions )
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197 },
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198 #else
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199 }
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200 #end if
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201 #end for
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202 #if len( $conditions ) > 1
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203 #if str( $rule_configuration.rules_selector ) == "True":
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204 ],
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205 "rule" : "${rule_configuration.rules}"
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206 #else
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207 ]
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208 #end if
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209 }
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210 #end if
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211 </configfile>
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212 </configfiles>
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213
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214 <outputs>
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215 <data format="txt" name="out_file2" />
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216 <data format="bam" name="out_file1" />
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217 </outputs>
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218 <tests>
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219 <test>
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220 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
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221 <param name="bam_property_selector" value="mapQuality"/>
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222 <param name="bam_property_value" value=">20"/>
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223 <output name="out_file1" file="bamtools-test1.bam" ftype="bam"/>
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224 </test>
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225 </tests>
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226 <help>
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227 **What is does**
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228
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229 BAMTools filter is a very powerful utility to perform complex filtering of BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).
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230
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231 -----
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232
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233 **How it works**
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234
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235 The tool use logic relies on the three concepts: (1) input BAM, (2) groups, and (3) filters.
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236
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237 *Input BAM(s)*
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238
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239 The input BAM is self-explanatory. This is the dataset you will be filtering. The tool can accept just one or multiple BAM files. To filter on multiple BAMs just add them by clicking **Add new BAM dataset(s) to filter**
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240
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241 *Conditions and Filters*
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242
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243 Conditions for filtering BAM files can be arranged in **Groups and Filters**. While it can be confusing at first this is what gives ultimate power to this tools. So try to look at the examples we are supplying below.
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244
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245 -----
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246
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247 **Example 1. Using a single filter**
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248
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249 When filtering on a single condition there is no need to worry about filters and conditions. Just choose a filter from the **Select BAM property to filter on:** dropdown and enter a value (or click a checkbox for binary filters).
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250 For example, for retaining reads with mapping quality of at least 20 one would set the tool interface as shown below:
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251
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252 .. image:: images/simple-filter.png
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253
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254 -----
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255
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256 **Example 2. Using multiple filters**
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257
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258 Now suppose one needs to extract reads that (1) have mapping quality of at least 20, (2) contain at least 1 mismatch, and (3) are mapping onto forward strand only.
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259 To do so we will use three filters as shown below (multiple filters are added to the interface by clicking on the **Add new Filter** button):
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260
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261 .. image:: images/multiple-filters.png
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262
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263 In this case (you can see that the three filters are grouped within a single Condition - **Condition 1**) the filter too use logical **AND** to perform filtering.
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264 In other words only reads that (1) have mapping quality of at least 20 **AND** (2) contain at least 1 mismatch **AND** are mapping onto forward strand will be returned in this example.
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265
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266 -----
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267
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268 **Example 3. Complex filtering with multiple conditions**
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269
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270 Suppose now you would like to select **either** reads that (**1**) have (*1.1*) no mismatches and (*1.2*) are on the forward strand **OR** (**2**) reads that have (*2.1*)
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271 at least one mismatch and (*2.2*) are on the reverse strand. In this scenario we have to set up two conditions: (**1**) and (**2**) each with two filters: *1.1* and *1.2* as well as *2.1* and *2.2*.
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272 The following screenshot expalins how this can be done:
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273
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274 .. image:: images/complex-filters.png
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275
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276 -----
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277
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278 **Example 4. Even more complex filtering with Rules**
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279
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280 In the above example we have used two conditions (Condition 1 and Condition 2). Using multiple conditions allows to combine them and a variety of ways to enable even more powerful filtering.
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281 For example, suppose get all reads that (**1**) do NOT map to mitochondria and either (**2**) have mapping quality over 20, or (**3**) are in properly mapped pairs. The logical rule to enable such
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282 filtering will look like this::
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283
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284 !(1) & (2 | 3)
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285
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286 Here, numbers 1, 2, and 3 represent conditions. The following screenshot illustrates how to do this in Galaxy:
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287
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288 .. image:: images/rule.png
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289
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290 There are three conditions here, each with a single filter. A text entry area that can be opened by clicking on the **Would you like to set rules?** checkbox enables you to enter a rule.
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291 Here numbers correspond to numbers of conditions as they are shown in the interface. E.g., 1 corresponds to condition 1, 2 to condition 2 and so on... In human language this means::
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292
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293 NOT condition 1 AND (condition 2 OR condition 3)
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294
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295 -----
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296
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297 **JSON script file**
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298
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299 This tool produces two outputs. One of the them is a BAM file containing filtered reads. The other is a JSONified script. It can help you to see how your instructions are sent to BAMTools.
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300 For instance, the example 4 looks like this in the JSON form::
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301
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302 {
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303 "filters":
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304 [
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305 { "id": "1",
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306 "tag":"NM:=0",
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307 "isReverseStrand":"false"
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308 },
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309 { "id": "2",
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310 "tag":"NM:>0",
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311 "isReverseStrand":"true"
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312 }
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313 ]
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314 }
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315
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316
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317
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318 -----
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319
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320 **More information**
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321
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322 .. class:: infomark
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323
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324 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
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325
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326
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327 </help>
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328 </tool>
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