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1 <tool name="FilterSamReads" id="picard_FilterSamReads" version="1.126.0">
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2 <description>include or exclude aligned and unaligned reads and read lists</description>
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3 <requirements>
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4 <requirement type="package" version="1.126.0">picard</requirement>
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5 </requirements>
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6
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7 <macros>
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8 <import>picard_macros.xml</import>
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9 </macros>
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10
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11 <command>
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12 @java_options@
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13
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14 ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order
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15
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16 java -jar \$JAVA_JAR_PATH/picard.jar
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17 SortSam
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18 INPUT="${inputFile}"
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19 OUTPUT=query_sorted_bam.bam
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20 SORT_ORDER=queryname
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21 VALIDATION_STRINGENCY=LENIENT
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22 QUIET=true
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23 VERBOSITY=ERROR
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24
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25 &&
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26
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27 java -jar \$JAVA_JAR_PATH/picard.jar
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28 FilterSamReads
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29 INPUT=query_sorted_bam.bam
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30 FILTER="${filter_type.filter}"
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31
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32 #if ( str( $filter_type.filter ) == "includeReadList" or str( $filter_type.filter ) == "excludeReadList" ):
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33 READ_LIST_FILE="${filter_type.read_list_file}"
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34 #end if
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35
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36 OUTPUT="${outFile}"
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37 SORT_ORDER=coordinate
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38 VALIDATION_STRINGENCY="${validation_stringency}"
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39 QUIET=true
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40 VERBOSITY=ERROR
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41
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42 </command>
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43 <inputs>
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44 <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
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45 <conditional name="filter_type">
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46 <param name="filter" type="select" label="Select filtering type" help="FILTER; see Help for deatiled info">
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47 <option value="includeAligned">Include aligned</option>
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48 <option value="excludeAligned">Exclude aligned</option>
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49 <option value="includeReadList">Include read list</option>
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50 <option value="excludeReadList">Exclude read list</option>
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51 </param>
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52 <when value="includeAligned"/> <!-- do nothing -->
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53 <when value="excludeAligned"/> <!-- do nothing -->
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54 <when value="includeReadList">
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55 <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be INCLUDED in the output" help="READ_LIST_FILE"/>
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56 </when>
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57 <when value="excludeReadList">
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58 <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be EXCLUDED in the output" help="READ_LIST_FILE"/>
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59 </when>
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60 </conditional>
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61
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62 <expand macro="VS" />
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63
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64 </inputs>
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65
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66 <outputs>
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67 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: filtered BAM"/>
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68 </outputs>
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69
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70 <tests>
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71 <test>
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72 <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
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73 <param name="filter" value="includeReadList"/>
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74 <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
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75 <param name="validation_stringency" value="LENIENT"/>
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76 <output name="outFile" file="picard_FilterSamReads_include_reads_test1.bam" ftype="bam" lines_diff="2"/>
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77 </test>
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78 <test>
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79 <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
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80 <param name="filter" value="excludeReadList"/>
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81 <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
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82 <param name="validation_stringency" value="LENIENT"/>
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83 <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="2"/>
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84 </test>
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85 </tests>
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86
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87 <stdio>
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88 <exit_code range="1:" level="fatal"/>
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89 </stdio>
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90
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91 <help>
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92
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93 **Purpose**
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94
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95 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
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96
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97 ------
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98
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99 .. class:: warningmark
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100
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101 **Warning on using this tool on BWA-MEM output**
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102
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103 This tool will likely fail on BAM datasets generated by BWA MEM as it generates partial read alignemnts.
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104
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105 @dataset_collections@
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106
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107 @description@
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108
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109 FILTER=Filter Filter. Required. Possible values:
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110 includeAligned [OUTPUT SAM/BAM will contain aligned
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111 reads only. (Note that *both* first and
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112 second of paired reads must be aligned to be included
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113 in the OUTPUT SAM or BAM)],
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114
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115 excludeAligned [OUTPUT SAM/BAM will contain un-mapped reads only.
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116 (Note that *both* first and second of pair must be aligned to be
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117 excluded from the OUTPUT SAM or BAM)]
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118
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119 includeReadList [OUTPUT SAM/BAM will contain reads
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120 that are supplied in the READ_LIST_FILE file]
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121
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122 excludeReadList [OUTPUT bam will contain
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123 reads that are *not* supplied in the READ_LIST_FILE file]}
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124
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125 READ_LIST_FILE=File
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126 RLF=File Read List File containing reads that will be included or excluded from the OUTPUT SAM or
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127 BAM file. Default value: null.
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128
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129 @more_info@
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130
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131 </help>
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132 </tool>
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133
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134
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