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1 <tool name="MergeBamAlignment" id="picard_MergeBamAlignment" version="1.126.0">
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2 <description>merge alignment data with additional info stored in an unmapped BAM dataset</description>
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3 <requirements><requirement type="package" version="1.126.0">picard</requirement></requirements>
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4
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5 <macros>
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6 <import>picard_macros.xml</import>
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7 </macros>
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8
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9 <command>
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10 @java_options@
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11 #set $picard_dict = "localref.dict"
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12 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension
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13
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14 ln -s "${reference_source.ref_file}" "${ref_fasta}" &&
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15
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16 #if str( $reference_source.reference_source_selector ) == "history":
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17
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18 java -jar \$JAVA_JAR_PATH/picard.jar CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
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19 QUIET=true
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20 VERBOSITY=ERROR
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21
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22 &&
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23
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24 #else:
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25
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26 #set $ref_fasta = str( $reference_source.ref_file.fields.path )
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27
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28 #end if
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29
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30 java -jar \$JAVA_JAR_PATH/picard.jar
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31 MergeBamAlignment
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32 UNMAPPED_BAM="${unmapped_bam}"
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33
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34 PAIRED_RUN=true ##This argument is ignored and will be removed. Required. Possible values: {true, false}
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35
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36 #if str( $aligned_or_read1_and_read2.aligned_or_read1_and_read2_selector ) == "paired_one_file":
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37 #for $dataset in $aligned_or_read1_and_read2.aligned_bams:
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38 ALIGNED_BAM="${dataset.aligned_bam}"
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39 #end for
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40 #elif str( $aligned_or_read1_and_read2.aligned_or_read1_and_read2_selector ) == "paired_two_files":
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41 #for $dataset in $aligned_or_read1_and_read2.read1_aligned_bams:
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42 READ1_ALIGNED_BAM="${dataset.read1_aligned_bam}"
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43 #end for
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44 #for $dataset in $aligned_or_read1_and_read2.read2_aligned_bams:
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45 READ2_ALIGNED_BAM="${dataset.read1_aligned_bam}"
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46 #end for
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47 #else
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48 #for $dataset in $aligned_or_read1_and_read2.read1_aligned_bams:
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49 READ1_ALIGNED_BAM="${dataset.read1_aligned_bam}"
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50 #end for
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51 #end if
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52
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53 OUTPUT="${outFile}"
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54 REFERENCE_SEQUENCE="${ref_fasta}"
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55
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56 CLIP_ADAPTERS="${clip_adapters}"
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57 IS_BISULFITE_SEQUENCE="${is_bisulfite_sequence}"
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58 ALIGNED_READS_ONLY="${aligned_reads_only}"
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59 MAX_INSERTIONS_OR_DELETIONS="${max_insertions_or_deletions}"
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60
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61 #for $attribute in $attributes_to_retain:
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62 ATTRIBUTES_TO_RETAIN="${$attribute.attribute}"
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63 #end for
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64
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65 #for $attribute in $attributes_to_remove:
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66 ATTRIBUTES_TO_REMOVE="${$attribute.attribute}"
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67 #end for
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68
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69 READ1_TRIM="${read1_trim}"
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70 READ2_TRIM="${read2_trim}"
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71
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72 #if str( $orientations ) != "None":
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73 #for $orientation in str( $orientations ).split(','): ## See trello card https://trello.com/c/9nW02Zhd
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74 EXPECTED_ORIENTATIONS="${orientation}"
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75 #end for
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76 #end if
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77
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78 ALIGNER_PROPER_PAIR_FLAGS="${aligner_proper_pair_flags}"
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79 PRIMARY_ALIGNMENT_STRATEGY="${primary_alignment_strategy}"
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80 CLIP_OVERLAPPING_READS="${clip_overlapping_reads}"
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81 INCLUDE_SECONDARY_ALIGNMENTS="${include_secondary_alignments}"
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82 ADD_MATE_CIGAR="${add_mate_cigar}"
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83
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84 VALIDATION_STRINGENCY="${validation_stringency}"
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85
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86 SORT_ORDER=coordinate
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87 QUIET=true
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88 VERBOSITY=ERROR
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89
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90 </command>
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91
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92 <inputs>
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93
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94 <conditional name="reference_source">
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95 <param name="reference_source_selector" type="select" label="Load reference genome from">
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96 <option value="cached">Local cache</option>
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97 <option value="history">History</option>
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98 </param>
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99 <when value="cached">
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100 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
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101 <options from_data_table="picard_indexes">
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102 <filter type="sort_by" column="2" />
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103 <validator type="no_options" message="No indexes are available" />
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104 </options>
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105 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
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106 </param>
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107 </when>
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108 <when value="history">
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109 <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" />
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110 </when>
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111 </conditional>
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112
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113 <param format="sam,bam" name="unmapped_bam" type="data" label="Selected unaligned SAM or BAM with original reads" help="UNMAPPED_BAM; This dataset must be sorted in queryname order (use picard_SortSam to do this)" />
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114 <conditional name="aligned_or_read1_and_read2">
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115 <param name="aligned_or_read1_and_read2_selector" type="select" label="What type of aligned data do you have?">
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116 <option value="paired_one_file">Paired data in a single BAM file (ALIGNED_BAM)</option>
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117 <option value="paired_two_files">Paired data in separate files (READ1_ALIGNED_BAM and READ2_ALIGNED_BAM)</option>
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118 <option value="single_file">Singe end data (READ1_ALIGNED_BAM)</option>
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119 </param>
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120 <when value="paired_one_file">
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121 <repeat name="aligned_bams" title="Aligned SAM or BAM dataset" min="1" help="You can provide multiple datasets">
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122 <param name="aligned_bam" type="data" format="sam,bam" label="SAM or BAM dataset(s) with alignment data" help="ALIGNED_BAM"/>
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123 </repeat>
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124 </when>
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125 <when value="paired_two_files">
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126 <repeat name="read1_aligned_bams" title="Aligned SAM or BAM dataset for Read 1" min="1" help="You can provide multiple datasets">
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127 <param name="read1_aligned_bam" type="data" format="sam,bam" label="SAM or BAM dataset(s) with alignment data for Read1" help="READ1_ALIGNED_BAM"/>
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128 </repeat>
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129 <repeat name="read2_aligned_bams" title="Aligned SAM or BAM dataset for Read 2" min="1" help="You can provide multiple datasets">
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130 <param name="read2_aligned_bam" type="data" format="sam,bam" label="SAM or BAM dataset(s) with alignment data for Read2" help="READ2_ALIGNED_BAM"/>
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131 </repeat>
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132 </when>
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133 <when value="single_file">
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134 <repeat name="read1_aligned_bams" title="Aligned SAM or BAM dataset for Single Reads" min="1" help="You can provide multiple datasets">
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135 <param name="read1_aligned_bam" type="data" format="sam,bam" label="SAM or BAM dataset(s) with alignment data" help="READ1_ALIGNED_BAM"/>
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136 </repeat>
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137 </when>
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138 </conditional>
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139
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140 <param name="clip_adapters" type="boolean" checked="true" label="Whether to clip adapters where identified" help="CLIP_ADAPTERS; default=True"/>
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141 <param name="is_bisulfite_sequence" type="boolean" label="Whether the data is from bisulfite sequencing (used when caculating the NM tag)" help="IS_BISULFITE_SEQUENCE; default=False"/>
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142 <param name="aligned_reads_only" type="boolean" label="Whether to output only aligned reads" help="ALIGNED_READS_ONLY; default=False"/>
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143 <param name="max_insertions_or_deletions" type="integer" value="1" label="The maximum number of insertions or deletions permitted for an alignment to be included" help="MAX_INSERTIONS_OR_DELETIONS; Alignments with more than this many insertions or deletions will be ignored. Set to -1 to allow any number of insertions or deletions. default=1"/>
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144
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145 <repeat name="attributes_to_retain" title="Retain the following alignment attribute" min="0" help="You can provide multiple attributes">
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146 <param name="attribute" type="text" size="4" label="Reserved alignment attributes (tags starting with X, Y, or Z) that should be brought over from the alignment data when merging" help="ATTRIBUTES_TO_RETAIN; example: XA"/>
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147 </repeat>
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148
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149 <repeat name="attributes_to_remove" title="Remove the following alignment attribute" min="0" help="You can provide multiple attributes">
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150 <param name="attribute" type="text" size="4" label="Attributes from the alignment record that should be removed when merging." help="ATTRIBUTES_TO_REMOVE; This overrides ATTRIBUTES_TO_RETAIN if they share common tags"/>
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151 </repeat>
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152
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153 <param name="read1_trim" type="integer" value="0" label="The number of bases trimmed from the beginning of read 1 prior to alignment" help="READ1_TRIM; default=0"/>
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154 <param name="read2_trim" type="integer" value="0" label="The number of bases trimmed from the beginning of read 2 prior to alignment" help="READ2_TRIM; default=0"/>
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155
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156 <param name="orientations" type="select" multiple="True" display="checkboxes" label="The expected orientation of proper read pairs" help="EXPECTED_ORIENTATIONS; multiple orinetations can be selected">
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157 <option value="FR">Forward/Reverse (FR)</option>
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158 <option value="RF">Reverse/Forward (RF)</option>
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159 <option value="TANDEM">Tandem</option>
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160 </param>
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161
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162
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163 <param name="aligner_proper_pair_flags" type="boolean" label="Use the aligner's idea of what a proper pair is rather than computing in this program" help="ALIGNER_PROPER_PAIR_FLAGS; default=False"/>
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164
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165 <param name="primary_alignment_strategy" type="select" label="Strategy for selecting primary alignment when the aligner has provided more than one alignment for a pair or fragments" help="PRIMARY_ALIGNMENT_STRATEGY; see help below for more info; default=BestMapq">
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166 <option value="BestMapq" selected="True">BestMapq</option>
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167 <option value="EarliestFragment">EarliestFragment</option>
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168 <option value="BestEndMapq">BestEndMapq</option>
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169 <option value="MostDistant">MostDistant</option>
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170 </param>
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171
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172 <param name="clip_overlapping_reads" type="boolean" checked="True" label="For paired reads, soft clip the 3' end of each read if necessary so that it does not extend past the 5' end of its mate" help="CLIP_OVERLAPPING_READS; default=True"/>
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173 <param name="include_secondary_alignments" type="boolean" checked="True" label="If false, do not write secondary alignments to output" help="INCLUDE_SECONDARY_ALIGNMENTS; default=True"/>
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174 <param name="add_mate_cigar" type="boolean" checked="True" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/>
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175 <expand macro="VS" />
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176 </inputs>
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177 <outputs>
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178 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with merged alignments"/>
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179 </outputs>
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180 <tests>
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181 <test>
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182 <param name="reference_source_selector" value="history" />
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183 <param name="ref_file" value="picard_MergeBamAlignment_ref.fa" ftype="fasta" />
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184 <param name="unmapped_bam" value="picard_MergeBamAlignment_unaligned.bam" ftype="bam"/>
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185 <param name="aligned_or_read1_and_read2_selector" value="paired_one_file"/>
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186 <param name="aligned_bam" value="picard_MergeBamAlignment_aligned.bam" ftype="bam"/>
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187 <param name="clip_adapters" value="True"/>
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188 <param name="is_bisulfite_sequence" value="False"/>
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189 <param name="aligned_reads_only" value="False"/>
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190 <param name="max_insertions_or_deletions" value="1"/>
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191 <param name="read1_trim" value="0"/>
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192 <param name="read2_trim" value="0"/>
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193 <param name="orientation" value="FR"/>
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194 <param name="aligner_proper_pair_flags" value="False"/>
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195 <param name="primary_alignment_strategy" value="BestMapq"/>
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196 <param name="clip_overlapping_reads" value="True"/>
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197 <param name="include_secondary_alignments" value="True"/>
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198 <param name="add_mate_cigar" value="True"/>
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199 <output name="outFile" file="picard_MergeBamAlignment_test1.bam" ftype="bam" lines_diff="2"/>
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200 </test>
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201 </tests>
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202
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203 <stdio>
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204 <exit_code range="1:" level="fatal"/>
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205 </stdio>
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206
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207 <help>
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208
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209 .. class:: infomark
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210
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211 **Purpose**
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212
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213 Merges alignment data from a SAM or BAM dataset with additional data stored in an unmapped BAM dataset and produces a third SAM or BAM dataset of aligned and unaligned reads.
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214
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215 @dataset_collections@
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216
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217 @description@
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218
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219 UNMAPPED_BAM=File
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220 UNMAPPED=File Original SAM or BAM file of unmapped reads, which must be in queryname order. Required.
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221
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222 ALIGNED_BAM=File
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223 ALIGNED=File SAM or BAM file(s) with alignment data. This option may be specified 0 or more times.
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224 Cannot be used in conjuction with option(s) READ1_ALIGNED_BAM (R1_ALIGNED)
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225 READ2_ALIGNED_BAM (R2_ALIGNED)
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226
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227 READ1_ALIGNED_BAM=File
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228 R1_ALIGNED=File SAM or BAM file(s) with alignment data from the first read of a pair. This option may be
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229 specified 0 or more times. Cannot be used in conjuction with option(s) ALIGNED_BAM
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230 (ALIGNED)
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231
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232 READ2_ALIGNED_BAM=File
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233 R2_ALIGNED=File SAM or BAM file(s) with alignment data from the second read of a pair. This option may
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234 be specified 0 or more times. Cannot be used in conjuction with option(s) ALIGNED_BAM
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235 (ALIGNED)
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236
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237 PAIRED_RUN=Boolean
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238 PE=Boolean This argument is ignored and will be removed. Required. Possible values: {true, false}
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239
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240 JUMP_SIZE=Integer
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241 JUMP=Integer The expected jump size (required if this is a jumping library). Deprecated. Use
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242 EXPECTED_ORIENTATIONS instead Default value: null. Cannot be used in conjuction with
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243 option(s) EXPECTED_ORIENTATIONS (ORIENTATIONS)
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244
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245 CLIP_ADAPTERS=Boolean Whether to clip adapters where identified. Default value: true. Possible values: {true, false}
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246
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247 IS_BISULFITE_SEQUENCE=Boolean Whether the lane is bisulfite sequence (used when caculating the NM tag). Default value:
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248 false. Possible values: {true, false}
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249
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250 ALIGNED_READS_ONLY=Boolean Whether to output only aligned reads. Default value: false. Possible values: {true, false}
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251
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252 MAX_INSERTIONS_OR_DELETIONS=Integer
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253 MAX_GAPS=Integer The maximum number of insertions or deletions permitted for an alignment to be included.
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254 Alignments with more than this many insertions or deletions will be ignored. Set to -1 to
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255 allow any number of insertions or deletions. Default value: 1.
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256
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257 ATTRIBUTES_TO_RETAIN=String Reserved alignment attributes (tags starting with X, Y, or Z) that should be brought over
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258 from the alignment data when merging. This option may be specified 0 or more times.
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259
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260 ATTRIBUTES_TO_REMOVE=String Attributes from the alignment record that should be removed when merging. This overrides
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261 ATTRIBUTES_TO_RETAIN if they share common tags. This option may be specified 0 or more
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262 times.
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263
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264 READ1_TRIM=Integer
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265 R1_TRIM=Integer The number of bases trimmed from the beginning of read 1 prior to alignment Default
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266 value: 0.
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267
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268 READ2_TRIM=Integer
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269 R2_TRIM=Integer The number of bases trimmed from the beginning of read 2 prior to alignment Default
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270 value: 0.
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271
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272 EXPECTED_ORIENTATIONS=PairOrientation
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273 ORIENTATIONS=PairOrientation The expected orientation of proper read pairs. Replaces JUMP_SIZE Possible values: {FR,
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274 RF, TANDEM} This option may be specified 0 or more times. Cannot be used in conjuction
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275 with option(s) JUMP_SIZE (JUMP)
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276
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277 ALIGNER_PROPER_PAIR_FLAGS=Boolean
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278 Use the aligner's idea of what a proper pair is rather than computing in this program.
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279 Default value: false. Possible values: {true, false}
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280
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281 SORT_ORDER=SortOrder
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282 SO=SortOrder The order in which the merged reads should be output. Default value: coordinate.
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283 Possible values: {unsorted, queryname, coordinate}
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284
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285 PRIMARY_ALIGNMENT_STRATEGY=PrimaryAlignmentStrategy
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286 Strategy for selecting primary alignment when the aligner has provided more than one
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287 alignment for a pair or fragment, and none are marked as primary, more than one is marked
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288 as primary, or the primary alignment is filtered out for some reason. BestMapq expects
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289 that multiple alignments will be correlated with HI tag, and prefers the pair of
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290 alignments with the largest MAPQ, in the absence of a primary selected by the aligner.
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291 EarliestFragment prefers the alignment which maps the earliest base in the read. Note
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292 that EarliestFragment may not be used for paired reads. BestEndMapq is appropriate for
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293 cases in which the aligner is not pair-aware, and does not output the HI tag. It simply
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294 picks the alignment for each end with the highest MAPQ, and makes those alignments
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295 primary, regardless of whether the two alignments make sense together.MostDistant is also
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296 for a non-pair-aware aligner, and picks the alignment pair with the largest insert size.
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297 If all alignments would be chimeric, it picks the alignments for each end with the best
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298 MAPQ. For all algorithms, ties are resolved arbitrarily. Default value: BestMapq.
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299 Possible values: {BestMapq, EarliestFragment, BestEndMapq, MostDistant}
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300
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301 CLIP_OVERLAPPING_READS=BooleanFor paired reads, soft clip the 3' end of each read if necessary so that it does not
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302 extend past the 5' end of its mate. Default value: true. Possible values: {true, false}
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303
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304 INCLUDE_SECONDARY_ALIGNMENTS=Boolean
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305 If false, do not write secondary alignments to output. Default value: true.
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306 Possible values: {true, false}
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307
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308 ADD_MATE_CIGAR=Boolean
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309 MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Possible values: {true, false}
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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_info@
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315 </help>
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316 </tool>
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317
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