Mercurial > repos > matthias > dada2_plotqualityprofile

annotate dada2_plotQualityProfile.xml @ 8:7970dfbedde3 draft

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author matthias
date Mon, 27 May 2019 13:23:01 -0400
parents ec0479593908
children d908015e5889
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1 <tool id="dada2_plotQualityProfile" name="dada2: plotQualityProfile" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@">
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2 <description>plot a visual summary of the quality scores</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ##name files by linking
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10 #import re
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11 #if "batch" in str($paired_cond.paired_select)
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12 #set elid = re.sub('[^\w\-\.]', '_', str($paired_cond.fl.element_identifier))
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13 #if "single" in str($paired_cond.paired_select)
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14 ln -s '$paired_cond.fl' '$elid' &&
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15 #else
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16 ln -s '$paired_cond.fl.forward' '$elid'_forward &&
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17 ln -s '$paired_cond.fl.reverse' '$elid'_reverse &&
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18 #end if
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19 #else
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20 #for $read in $paired_cond.fl:
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21 #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
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22 #if "single" in str($paired_cond.paired_select)
863ebf0d28d5 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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23 ln -s '$read' '$elid' &&
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24 #else
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25 ln -s '$read.forward' '$elid'_forward &&
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26 ln -s '$read.reverse' '$elid'_reverse &&
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27 #end if
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28 #end for
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29 #end if
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31 Rscript --slave '$dada2_script'
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32 ]]></command>
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33 <configfiles>
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34 <configfile name="dada2_script"><![CDATA[
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35 #import re
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36 fwd_files = c()
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37 rev_files = c()
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38 #if "batch" in str($paired_cond.paired_select)
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39 #set elid = re.sub('[^\w\-\.]', '_', str($paired_cond.fl.element_identifier))
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40 #if "single" in str($paired_cond.paired_select)
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41 fwd_files = c(fwd_files, '$elid')
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42 #else
8
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43 fwd_files = c(fwd_files, paste('$elid', 'forward', sep = "_"))
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44 rev_files = c(rev_files, paste('$elid', 'reverse', sep = "_"))
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45 #end if
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46 #else
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47 #for $read in $paired_cond.fl:
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48 #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
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49 #if "single" in str($paired_cond.paired_select)
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50 fwd_files = c(fwd_files, '$elid')
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51 #else
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52 fwd_files = c(fwd_files, paste('$elid', 'forward', sep = "_"))
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53 rev_files = c(rev_files, paste('$elid', 'reverse', sep = "_"))
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54 #end if
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55 #end for
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56 #end if
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57
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58 #if not "batch" in str($paired_cond.paired_select)
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59 agg = $paired_cond.aggregate
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60 #else
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61 agg = FALSE
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62 #end if
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63
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64 library(ggplot2, quietly=T)
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65 library(dada2, quietly=T)
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66
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67 qp <- plotQualityProfile(fwd_files,
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68 #if str($n) != ""
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69 n=$n,
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70 #end if
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71 aggregate = agg)
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72 ggsave('output.pdf', qp, width = 20,height = 15,units = c("cm"))
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73
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74 #if "paired" in str($paired_cond.paired_select)
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75 qp <- plotQualityProfile(rev_files,
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76 #if str($n) != ""
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77 n=$n,
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78 #end if
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79 aggregate = agg)
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80 ggsave('output_rev.pdf', qp, width = 20,height = 15,units = c("cm"))
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81 #end if
0
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82 ]]></configfile>
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83 </configfiles>
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84 <inputs>
3
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85 <conditional name="paired_cond">
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86 <param name="paired_select" type="select" label="Input data organisation and processing mode" help="Select if data is organized in a paired collection or not (note that the pairing of the data sets is not used by the tool); batch will create a separate pdf for each input data set or data set pair; non-batch will create one pdf containing a plot for each data set">
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87 <option value="paired">paired - non batch</option>
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88 <option value="single">single - non batch</option>
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89 <option value="paired_batch">paired - batch</option>
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90 <option value="single_batch">single - batch</option>
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91 </param>
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92 <when value="paired">
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93 <param argument="fl" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz" label="Short read data"/>
8
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94 <param argument="aggregate" type="boolean" label="Aggregate data" checked="True" truevalue="TRUE" falsevalue="FALSE" help="Create a single plot for all data sets (default) or a separate plot for each data set"/>
3
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95 </when>
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96 <when value="single">
7
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97 <param argument="fl" type="data" multiple="true" format="fastq,fastq.gz" label="Short read data"/>
8
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98 <param argument="aggregate" type="boolean" label="Aggregate data" checked="True" truevalue="TRUE" falsevalue="FALSE" help="Create a single plot for all data sets (default) or a separate plot for each data set"/>
3
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99 </when>
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100 <when value="paired_batch">
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101 <param argument="fl" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Short read data"/>
3
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102 </when>
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103 <when value="single_batch">
7
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104 <param argument="fl" type="data" format="fastq,fastq.gz" label="Short read data"/>
3
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105 </when>
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106 </conditional>
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107 <param argument="n" type="integer" value="500000" label="sample number" help="number of records to sample from the fastq file"/>
0
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108 </inputs>
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109 <outputs>
8
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110 <data name="output" format="pdf" from_work_dir="output.pdf">
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111 <filter>"single" in paired_cond['paired_select']</filter>
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112 </data>
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113 <data name="output_fwd" format="pdf" from_work_dir="output.pdf" label="${tool.name} on ${on_string}: forward reads">
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114 <filter>"paired" in paired_cond['paired_select']</filter>
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115 </data>
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116 <data name="output_rev" format="pdf" from_work_dir="output_rev.pdf" label="${tool.name} on ${on_string}: reverse reads">
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117 <filter>"paired" in paired_cond['paired_select']</filter>
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118 </data>
0
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119 </outputs>
2
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120 <tests>
3
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121 <!-- paired non-batch, aggregate -->
2
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122 <test>
3
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123 <param name="paired_cond|paired_select" value="paired"/>
8
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124 <param name="paired_cond|aggregate" value="TRUE"/>
5
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125 <param name="paired_cond|fl">
3
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126 <collection type="list:paired">
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127 <element name="F3D0_S188_L001">
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128 <collection type="paired">
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129 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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130 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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131 </collection>
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132 </element>
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133 </collection>
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134 </param>
8
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135 <output name="output_fwd" value="qualityProfileMultiple.pdf" ftype="pdf"/>
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136 <output name="output_rev" value="qualityProfileMultiple_rev.pdf" ftype="pdf"/>
2
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137 </test>
3
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138 <!-- paired, batch, no aggregate-->
2
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139 <test>
3
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140 <param name="paired_cond|paired_select" value="paired_batch"/>
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141 <param name="paired_cond|fl">
3
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142 <collection type="paired">
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143 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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144 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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145 </collection>
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146 </param>
8
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147 <output name="output_fwd" value="qualityProfile.pdf" ftype="pdf"/>
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148 <output name="output_rev" value="qualityProfile_rev.pdf" ftype="pdf"/>
2
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149 </test>
3
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150 <!-- single, non-batch, aggregate -->
2
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151 <test>
3
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152 <param name="paired_cond|paired_select" value="single"/>
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153 <param name="paired_cond|aggregate" value="TRUE"/>
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154 <param name="paired_cond|fl" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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155 <param name="n" value="10000"/>
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156 <output name="output" value="qualityProfileSmallSample.pdf" ftype="pdf"/>
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157 </test>
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158 <!-- single, batch, no aggregate -->
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159 <test>
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160 <param name="aggregate" value="FALSE"/>
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161 <param name="paired_cond|paired_select" value="single_batch"/>
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162 <param name="paired_cond|fl" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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163 <param name="n" value="10000"/>
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164 <output name="output" value="qualityProfileSmallSample.pdf" ftype="pdf" compare="sim_size"/>
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165 </test> </tests>
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166 <help><![CDATA[
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167 Summary
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168 .......
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169
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170 This function plots a visual summary of the distribution of quality scores as a function of sequence position for the input fastq datasets.
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171
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172 Details
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173 .......
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174
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175 The distribution of quality scores at each position is shown as a grey-scale heat map, with dark colors corresponding to higher frequency. The plotted lines show positional summary statistics: green is the mean, orange is the median, and the dashed orange lines are the 25th and 75th quantiles. If the sequences vary in length, a red line will be plotted showing the percentage of reads that extend
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176 to at least that position.
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177
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178 Note this tool ignores the pairing of the reads, but the data is just processed as list.
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179 ]]></help>
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180 <expand macro="citations"/>
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181 </tool>