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annotate picard_FastqToSam.xml @ 26:fc3866ddc7b6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 0244aa33464cc27d1ce881cb310b8eda36e9a89c
author iuc
date Mon, 22 Aug 2022 09:54:37 +0000
parents 3b55709c0a01
children c943f4a04af0
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3b55709c0a01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 1ef1c65fa4d78e1332411af1999862d5a8f28125"
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1 <tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="20.01">
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2 <description>convert Fastq data into unaligned BAM</description>
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3 <macros>
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4 <import>picard_macros.xml</import>
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5 <token name="@WRAPPER_VERSION@">2</token>
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6 </macros>
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7 <xrefs>
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8 <xref type="bio.tools">picard_fastqtosam</xref>
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9 </xrefs>
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10 <expand macro="requirements" />
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11 <command detect_errors="exit_code"><![CDATA[
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12 @java_options@
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13 #if str( $input_type.input_type_selector ) == "se":
3b55709c0a01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 1ef1c65fa4d78e1332411af1999862d5a8f28125"
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14 #set fwd = $input_type.fastq
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15 #set rev = None
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16 #elif str( $input_type.input_type_selector ) == "pe":
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17 #set fwd = $input_type.fastq
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18 #set rev = $input_type.fastq2
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19 #else
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20 #set fwq = $input_type.fastq.forward
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21 #set rev = $input_type.fastq.reverse
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22 #end if
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23
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24 #if $fwd.ext.endswith(".gz")
3b55709c0a01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 1ef1c65fa4d78e1332411af1999862d5a8f28125"
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25 gunzip -c '$fwd' > fwd.fastq &&
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26 #else
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27 ln -s '$fwd' fwd.fastq &&
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28 #end if
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29 #if rev
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30 #if rev.ext.endswith(".gz")
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31 gunzip -c '$rev' > rev.fastq &&
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32 #else
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33 ln -s '$rev' rev.fastq &&
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34 #end if
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35 #end if
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36
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37 picard
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38 FastqToSam
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39
25
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40 FASTQ=fwd.fastq
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41 #if rev
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42 FASTQ2=rev.fastq
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43 #end if
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44
25
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45 #if $fwd.ext.startswith("fastqillumina")
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46 QUALITY_FORMAT="Illumina"
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47 #else if $fwd.ext.startswith("fastqsolexa")
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48 QUALITY_FORMAT="Solexa"
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49 #else
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50 QUALITY_FORMAT="Standard"
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51 #end if
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52 OUTPUT="${outFile}"
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53 READ_GROUP_NAME="${read_group_name}"
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54 SAMPLE_NAME="${sample_name}"
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55
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56 #if str( $library_name ):
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57 LIBRARY_NAME="${library_name}"
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58 #end if
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59
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60 #if str( $platform_unit ):
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61 PLATFORM_UNIT="${platform_unit}"
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62 #end if
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64 #if str( $platform ):
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65 PLATFORM="${platform}"
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66 #end if
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68 #if str( $sequencing_center ):
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69 SEQUENCING_CENTER="${sequencing_center}"
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70 #end if
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72 #if str( $predicted_insert_size ):
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73 PREDICTED_INSERT_SIZE="${predicted_insert_size}"
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74 #end if
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76 #if str( $comment ):
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77 COMMENT="${comment}"
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78 #end if
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80 #if str( $description ):
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81 DESCRIPTION="${description}"
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82 #end if
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83
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84 #if str( $run_date ):
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85 RUN_DATE="${run_date}"
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86 #end if
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88 MIN_Q="${min_q}"
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89 MAX_Q="${max_q}"
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90 STRIP_UNPAIRED_MATE_NUMBER="${strip_unpairied_mate_number}"
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91 ALLOW_AND_IGNORE_EMPTY_LINES="${allow_and_ignore_empty_lines}"
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92
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93 SORT_ORDER=coordinate
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94 VALIDATION_STRINGENCY="${validation_stringency}"
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95 QUIET=true
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96 VERBOSITY=ERROR
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97 @TMPDIR_OPTION@
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98 ]]></command>
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99 <inputs>
3
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100 <conditional name="input_type">
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101 <param name="input_type_selector" type="select" label="What is your input data" help="Select between single end, paired end, and collections. See help below for full explanation of dataset types">
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102 <option value="se">Single end (single dataset)</option>
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103 <option value="pe">Paired end (two datasets)</option>
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104 <option value="pc">Paired collection</option>
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105 </param>
3
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106 <when value="se">
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107 <param name="fastq" type="data" format="fastq,fastq.gz" label="Input fastq file for single end data" help="FASTQ"/>
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108 </when>
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109 <when value="pe">
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110 <param name="fastq" type="data" format="fastq,fastq.gz" label="Input fastq file for the first read in paired end data" help="FASTQ"/>
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111 <param name="fastq2" type="data" format="fastq,fastq.gz" label="Input fastq file for the second read of paired end data" help="FASTQ2"/>
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112 </when>
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113 <when value="pc">
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114 <param name="fastq" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="FASTQ paired dataset collection" help="FASTQ and FASTQ2; A collection of two datasets with forward and reverse reads. See help below on explanation of dataset collections"/>
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115 </when>
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116 </conditional>
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117
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118 <param name="read_group_name" type="text" value="A" label="Read group name" help="READ_GROUP_NAME"/>
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119 <param name="sample_name" type="text" value="sample-a" label="Sample name" help="SAMPLE_NAME"/>
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120 <param name="library_name" type="text" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/>
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121 <param name="platform_unit" type="text" optional="True" label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/>
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122 <param name="platform" type="text" optional="True" label="The platform type (e.g. illumina, 454)" help="PLATFORM; Optional"/>
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123 <param name="sequencing_center" type="text" optional="True" label="The sequencing center from which the data originated" help="SEQUENCING_CENTER; Optional"/>
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124
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125 <param name="predicted_insert_size" type="integer" min="0" max="100000" optional="True" label="Predicted median insert size, to insert into the read group header" help="PREDICTED_INSERT_SIZE; Optional"/>
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126 <param name="comment" type="text" optional="True" label="Comment to include in the output dataset's header" help="COMMENT; Optional"/>
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127 <param name="description" type="text" optional="True" label="Optional description information" help="DESCRIPTION; Optional"/>
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128 <param name="run_date" optional="True" type="text" label="Run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/>
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129 <param name="min_q" type="integer" value="0" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MIN_Q; An exception will be thrown if a quality is less than this value; default=0"/>
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130 <param name="max_q" type="integer" value="93" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MAX_Q; An exception will be thrown if a quality is greater than this value; default=93"/>
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131 <param name="strip_unpairied_mate_number" type="boolean" truevalue="true" falsevalue="false" label="If true and this is an unpaired fastq any occurance of '/1' will be removed from the end of a read name" help="STRIP_UNPAIRED_MATE_NUMBER; default=false"/>
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132 <param name="allow_and_ignore_empty_lines" type="boolean" truevalue="true" falsevalue="false" label="Allow (and ignore) empty lines" help="ALLOW_AND_IGNORE_EMPTY_LINES; default=false"/>
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133
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134 <expand macro="VS" />
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135
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136 </inputs>
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137
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138 <outputs>
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139 <data format="unsorted.bam" name="outFile" label="${tool.name} on ${on_string}: reads as unaligned BAM"/>
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140 </outputs>
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141
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142 <tests>
3
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143 <test>
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144 <param name="input_type_selector" value="pe" />
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145 <param name="read_group_name" value="A" />
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146 <param name="sample_name" value="sample-a" />
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147 <param name="library_name" value="A"/>
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148 <param name="platform_unit" value="A"/>
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149 <param name="platform" value="Illumina"/>
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150 <param name="sequencing_center" value="A"/>
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151 <param name="predicted_insert_size" value="300"/>
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152 <param name="comment" value="A"/>
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153 <param name="description" value="A"/>
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154 <param name="run_date" value="2014-10-10"/>
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155 <param name="min_q" value="0" />
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156 <param name="max_q" value="93" />
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157 <param name="strip_unpairied_mate_number" value="False" />
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158 <param name="allow_and_ignore_empty_lines" value="False" />
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159 <param name="validation_stringency" value="LENIENT"/>
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160 <param name="fastq" value="picard_FastqToSam_read1.fq.gz" ftype="fastq.gz" />
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161 <param name="fastq2" value="picard_FastqToSam_read2.fq.gz" ftype="fastq.gz" />
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162 <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="unsorted.bam" lines_diff="4"/>
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163 </test>
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164 </tests>
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165
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166 <help>
3
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167
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168 .. class:: infomark
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169
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170 **Purpose**
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171
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172 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
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173
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174 @dataset_collections@
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175
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176 @RG@
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177
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178 @description@
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179
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180 FASTQ=File
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181 F1=File Input fastq file for single end data, or first read in paired end
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182 data. Required.
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183
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184 FASTQ2=File
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185 F2=File Input fastq file for the second read of paired end data (if used).
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186
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187 QUALITY_FORMAT=FastqQualityFormat
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188 V=FastqQualityFormat A value describing how the quality values are encoded in the fastq. Either Solexa for
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189 pre-pipeline 1.3 style scores (solexa scaling + 66), Illumina for pipeline 1.3 and above
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190 (phred scaling + 64) or Standard for phred scaled scores with a character shift of 33.
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191 If this value is not specified, the quality format will be detected automatically.
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192 Default value: null. Possible values: {Solexa, Illumina, Standard}
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193
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194 READ_GROUP_NAME=String
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195 RG=String Read group name Default value: A.
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196
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197 SAMPLE_NAME=String
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198 SM=String Sample name to insert into the read group header Required.
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199
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200 LIBRARY_NAME=String
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201 LB=String The library name to place into the LB attribute in the read group header.
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202
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203 PLATFORM_UNIT=String
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204 PU=String The platform unit (often run_barcode.lane) to insert into the read group header.
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205
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206 PLATFORM=String
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207 PL=String The platform type (e.g. illumina, solid) to insert into the read group header.
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208
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209 SEQUENCING_CENTER=String
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210 CN=String The sequencing center from which the data originated.
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211
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212 PREDICTED_INSERT_SIZE=Integer
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213 PI=Integer Predicted median insert size, to insert into the read group header.
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214
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215 COMMENT=String
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216 CO=String Comment to include in the merged output file's header.
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217
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218 DESCRIPTION=String
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219 DS=String Inserted into the read group header.
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220
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221 RUN_DATE=Iso8601Date
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222 DT=Iso8601Date Date the run was produced, to insert into the read group header.
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223
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224 MIN_Q=Integer Minimum quality allowed in the input fastq. An exception will be thrown if a quality is
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225 less than this value. Default value: 0.
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226
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227 MAX_Q=Integer Maximum quality allowed in the input fastq. An exception will be thrown if a quality is
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228 greater than this value. Default value: 93.
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229
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230 STRIP_UNPAIRED_MATE_NUMBER=Boolean
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231 If true and this is an unpaired fastq any occurance of '/1' will be removed from the end
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232 of a read name. Default value: false. Possible values: {true, false}
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233
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234 ALLOW_AND_IGNORE_EMPTY_LINES=Boolean
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235 Allow (and ignore) empty lines Default value: false. Possible values: {true, false}
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236
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237
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238 @more_info@
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239
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240 </help>
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241 <expand macro="citations" />
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242 </tool>