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1 <tool name="FilterSamReads" id="picard_FilterSamReads" version="1.135">
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2 <description>include or exclude aligned and unaligned reads and read lists</description>
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3 <macros>
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4 <import>picard_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command>
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8 @java_options@
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9
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10 ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order
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11
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12 java -jar \$JAVA_JAR_PATH/picard.jar
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13 SortSam
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14 INPUT="${inputFile}"
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15 OUTPUT=query_sorted_bam.bam
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16 SORT_ORDER=queryname
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17 VALIDATION_STRINGENCY=LENIENT
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18 QUIET=true
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19 VERBOSITY=ERROR
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20
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21 &&
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22
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23 java -jar \$JAVA_JAR_PATH/picard.jar
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24 FilterSamReads
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25 INPUT=query_sorted_bam.bam
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26 FILTER="${filter_type.filter}"
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27
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28 #if ( str( $filter_type.filter ) == "includeReadList" or str( $filter_type.filter ) == "excludeReadList" ):
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29 READ_LIST_FILE="${filter_type.read_list_file}"
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30 #end if
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31
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32 OUTPUT="${outFile}"
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33 SORT_ORDER=coordinate
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34 VALIDATION_STRINGENCY="${validation_stringency}"
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35 QUIET=true
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36 VERBOSITY=ERROR
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37
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38 </command>
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39 <inputs>
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40 <param name="inputFile" 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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41 <conditional name="filter_type">
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42 <param name="filter" type="select" label="Select filtering type" help="FILTER; see Help for deatiled info">
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43 <option value="includeAligned">Include aligned</option>
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44 <option value="excludeAligned">Exclude aligned</option>
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45 <option value="includeReadList">Include read list</option>
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46 <option value="excludeReadList">Exclude read list</option>
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47 </param>
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48 <when value="includeAligned"/> <!-- do nothing -->
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49 <when value="excludeAligned"/> <!-- do nothing -->
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50 <when value="includeReadList">
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51 <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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52 </when>
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53 <when value="excludeReadList">
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54 <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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55 </when>
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56 </conditional>
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57
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58 <expand macro="VS" />
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59
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60 </inputs>
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61
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62 <outputs>
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63 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: filtered BAM"/>
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64 </outputs>
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65
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66 <tests>
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67 <test>
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68 <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
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69 <param name="filter" value="includeReadList"/>
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70 <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
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71 <param name="validation_stringency" value="LENIENT"/>
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72 <output name="outFile" file="picard_FilterSamReads_include_reads_test1.bam" ftype="bam" lines_diff="2"/>
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73 </test>
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74 <test>
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75 <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
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76 <param name="filter" value="excludeReadList"/>
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77 <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
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78 <param name="validation_stringency" value="LENIENT"/>
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79 <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="2"/>
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80 </test>
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81 </tests>
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82
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83 <stdio>
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84 <exit_code range="1:" level="fatal"/>
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85 </stdio>
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86
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87 <help>
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88
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89 **Purpose**
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90
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91 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
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92
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93 ------
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94
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95 .. class:: warningmark
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96
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97 **Warning on using this tool on BWA-MEM output**
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98
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99 This tool will likely fail on BAM datasets generated by BWA MEM as it generates partial read alignemnts.
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100
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101 @dataset_collections@
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102
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103 @description@
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104
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105 FILTER=Filter Filter. Required. Possible values:
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106 includeAligned [OUTPUT SAM/BAM will contain aligned
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107 reads only. (Note that *both* first and
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108 second of paired reads must be aligned to be included
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109 in the OUTPUT SAM or BAM)],
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110
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111 excludeAligned [OUTPUT SAM/BAM will contain un-mapped reads only.
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112 (Note that *both* first and second of pair must be aligned to be
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113 excluded from the OUTPUT SAM or BAM)]
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114
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115 includeReadList [OUTPUT SAM/BAM will contain reads
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116 that are supplied in the READ_LIST_FILE file]
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117
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118 excludeReadList [OUTPUT bam will contain
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119 reads that are *not* supplied in the READ_LIST_FILE file]}
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120
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121 READ_LIST_FILE=File
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122 RLF=File Read List File containing reads that will be included or excluded from the OUTPUT SAM or
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123 BAM file. Default value: null.
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124
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125 @more_info@
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126
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127 </help>
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128 </tool>
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129
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130
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