annotate bamtools-filter.xml @ 9:c20a4a4acf3f draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:04:29 -0500
parents 709d8669e8d6
children 4089f1be1a71
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c20a4a4acf3f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 <tool id="bamFilter" name="Filter" version="0.0.2">
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2 <description>BAM datasets 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 cat $script_file > $out_file2;
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8
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9 #for $bam_count, $input_bam in enumerate( $input_bams ):
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10 ln -s "${input_bam}" "localbam_${bam_count}.bam" &amp;&amp;
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11 ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp;
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12 #end for
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13
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14 bamtools
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15 filter
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16 -script $script_file
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17
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18 #for $bam_count, $input_bam in enumerate( $input_bams ):
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19 -in "localbam_${bam_count}.bam"
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20 #end for
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21 -out $out_file1
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22 </command>
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23 <inputs>
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24 <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/>
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25 <repeat name="conditions" title="Condition" min="1">
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26 <repeat name="filters" title="Filter" min="1">
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27 <conditional name="bam_property">
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28 <param name="bam_property_selector" type="select" label="Select BAM property to filter on">
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29 <option value="alignmentFlag"/>
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30 <option value="cigar"/>
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31 <option value="insertSize"/>
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32 <option value="isDuplicate"/>
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33 <option value="isFailedQC"/>
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34 <option value="isFirstMate"/>
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35 <option value="isMapped"/>
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36 <option value="isMateMapped"/>
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37 <option value="isMateReverseStrand"/>
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38 <option value="isPaired"/>
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39 <option value="isPrimaryAlignment"/>
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40 <option value="isProperPair"/>
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41 <option value="isReverseStrand"/>
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42 <option value="isSecondMate"/>
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43 <option selected="True" value="mapQuality"/>
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44 <option value="matePosition"/>
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45 <option value="mateReference"/>
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46 <option value="name"/>
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47 <option value="position"/>
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48 <option value="queryBases"/>
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49 <option value="reference"/>
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50 <option value="tag"/>
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51 </param>
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52 <!-- would be fanstastic to have AND and OR constructs in when statements -->
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53 <when value="alignmentFlag">
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54 <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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55 </when>
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56 <when value="cigar">
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57 <param name="bam_property_value" type="text" value="101M" label="Filter on this CIGAR string" help="Default (101M) is for 101 continuously matched bases"/>
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58 </when>
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59 <when value="insertSize">
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60 <param name="bam_property_value" type="text" value=">=250" label="Filter on inster size" help="You can use &gt;, &lt;, =, and ! (not) in your expression. E.g., to select pairs with inster size above 250 nt use &quot;>=250&quot;">
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61 <sanitizer invalid_char="">
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62 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
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63 </sanitizer>
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64 </param>
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65 </when>
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66 <when value="isDuplicate">
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67 <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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68 </when>
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69 <when value="isFailedQC">
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70 <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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71 </when>
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72 <when value="isFirstMate">
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73 <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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74 </when>
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75 <when value="isMapped">
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76 <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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77 </when>
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78 <when value="isMateMapped">
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79 <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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80 </when>
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81 <when value="isMateReverseStrand">
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82 <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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83 </when>
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84 <when value="isPaired">
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85 <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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86 </when>
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87 <when value="isPrimaryAlignment">
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88 <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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89 </when>
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90 <when value="isProperPair">
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91 <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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92 </when>
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93 <when value="isReverseStrand">
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94 <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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95 </when>
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96 <when value="isSecondMate">
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97 <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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98 </when>
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99 <when value="mapQuality">
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100 <param name="bam_property_value" type="text" value="20" label="Filter on read mapping quality (phred scale)" help="You can use &gt;, &lt;, =, and ! (not) in your expression. E.g., to select reads with mapping quality of at least 30 use &quot;>=30&quot;">
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101 <sanitizer invalid_char="">
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102 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
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103 </sanitizer>
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104 </param>
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105 </when>
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106 <when value="matePosition">
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107 <param name="bam_property_value" type="text" value="1000000" label="Filter on the position of the mate" help="You can use &gt;, &lt;, =, and ! (not) in your expression. E.g., to select reads with mate (second end) mapping after position 1,000,000 use &quot;&gt;1000000&quot;">
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108 <sanitizer invalid_char="">
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109 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
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110 </sanitizer>
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111 </param>
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112 </when>
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113 <when value="mateReference">
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114 <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 &quot;chr22&quot;">
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115 <sanitizer invalid_char="">
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116 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
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117 </sanitizer>
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118 </param>
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119 </when>
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120 <when value="name">
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121 <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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122 <sanitizer invalid_char="">
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123 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
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124 </sanitizer>
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125 </param>
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126 </when>
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127 <when value="position">
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128 <param name="bam_property_value" type="text" value="500000" label="Filter on the position of the read" help="You can use &gt;, &lt;, =, and ! (not) in your expression. E.g., to select reads mapping after position 5,000 use &quot;&gt;5000&quot;">
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129 <sanitizer invalid_char="">
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130 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
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131 </sanitizer>
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132 </param>
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133 </when>
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134 <when value="queryBases">
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135 <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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136 <sanitizer invalid_char="">
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137 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
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138 </sanitizer>
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139 </param>
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140 </when>
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141 <when value="reference">
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142 <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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143 <sanitizer invalid_char="">
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144 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
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145 </sanitizer>
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146 </param>
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147 </when>
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148 <when value="tag">
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149 <param name="bam_property_value" type="text" value="NM:&gt;1" label="Filter on a particular tag" help="You can use &gt;, &lt;, =, and ! (not).
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150 Tag name and its value must be separated by &quot;:&quot;. E.g., to obtain reads with at least one mismatch use &quot;NM:&gt;1&quot;">
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151 <sanitizer invalid_char="">
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152 <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value=":!="/></valid>
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153 </sanitizer>
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154 </param>
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155 </when>
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156 </conditional>
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157 </repeat>
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158 </repeat>
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159 <conditional name="rule_configuration">
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160 <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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161 <when value="true">
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162 <param name="rules" type="text" 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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163 <sanitizer invalid_char="">
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164 <valid initial="string.printable"/>
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165 </sanitizer>
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166 </param>
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167 </when>
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168 </conditional>
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169 </inputs>
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170
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171 <configfiles>
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172 <configfile name="script_file">
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173 ##Sets up a json configfile for bamtools filter
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174 ##If there is more than one condition prints brackets and "filters:"
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175 #if len( $conditions ) > 1
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176 {
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177 "filters":
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178 [
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179 #end if
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180 #for $i, $c in enumerate( $conditions, start=1 )
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181 { "id": "$i",
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182 #for $j, $s in enumerate( $c.filters, start=1 )
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183 ##The if below takes care of the comma at the end of last condition within group
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184 #if $j != len( $c.filters)
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185 "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}",
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186 #else
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187 "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}"
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188 #end if
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189 #end for
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190 ##The if below takes care of the comma at the end of last condition within group
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191 #if $i != len( $conditions )
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192 },
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193 #else
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194 }
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195 #end if
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196 #end for
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197 #if len( $conditions ) > 1
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198 #if str( $rule_configuration.rules_selector ) == "True":
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199 ],
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200 "rule" : "${rule_configuration.rules}"
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201 #else
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202 ]
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203 #end if
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204 }
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205 #end if
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206 </configfile>
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207 </configfiles>
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208
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209 <outputs>
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210 <data format="txt" name="out_file2" />
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211 <data format="bam" name="out_file1" />
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212 </outputs>
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213 <tests>
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214 <test>
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215 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
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216 <param name="bam_property_selector" value="mapQuality"/>
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217 <param name="bam_property_value" value=">20"/>
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218 <output name="out_file1" file="bamtools-test1.bam" ftype="bam"/>
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219 </test>
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220 </tests>
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221 <help>
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222 **What is does**
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223
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224 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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225
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226 -----
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227
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228 **How it works**
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229
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230 The tool use logic relies on the three concepts: (1) input BAM, (2) groups, and (3) filters.
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231
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232 *Input BAM(s)*
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233
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234 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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235
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236 *Conditions and Filters*
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237
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238 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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239
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240 -----
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241
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242 **Example 1. Using a single filter**
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243
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244 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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245 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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246
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247 .. image:: single-filter.png
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248
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249 -----
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250
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251 **Example 2. Using multiple filters**
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252
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253 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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254 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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255
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256 .. image:: multiple-filters.png
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257
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258 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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259 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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260
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261 -----
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262
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263 **Example 3. Complex filtering with multiple conditions**
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264
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265 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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266 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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267 The following screenshot expalins how this can be done:
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268
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269 .. image:: complex-filters.png
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270
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271 -----
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272
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273 **Example 4. Even more complex filtering with Rules**
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274
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275 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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276 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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277 filtering will look like this::
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278
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279 !(1) &amp; (2 | 3)
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280
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281 Here, numbers 1, 2, and 3 represent conditions. The following screenshot illustrates how to do this in Galaxy:
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282
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283 .. image:: rule.png
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284
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285 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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286 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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287
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288 NOT condition 1 AND (condition 2 OR condition 3)
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289
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290 -----
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291
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292 **JSON script file**
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293
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294 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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295 For instance, the example 4 looks like this in the JSON form::
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296
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297 {
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298 "filters":
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299 [
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300 { "id": "1",
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301 "tag":"NM:=0",
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302 "isReverseStrand":"false"
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303 },
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304 { "id": "2",
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305 "tag":"NM:>0",
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306 "isReverseStrand":"true"
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307 }
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308 ]
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309 }
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310
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311
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312 -----
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313
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314 **More information**
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315
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316 .. class:: infomark
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317
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318 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
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319
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320
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321 </help>
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322 <citations>
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323 <citation type="doi">10.1093/bioinformatics/btr174</citation>
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324 </citations>
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325 </tool>