Mercurial > repos > matthias > dada2_plotqualityprofile

annotate dada2_plotQualityProfile.xml @ 10:279014cdd101 draft

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author matthias
date Tue, 28 May 2019 12:47:08 -0400
parents d908015e5889
children 36224cf72a7b
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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 mkdir forward &&
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12 #if $batch_cond.paired_cond.paired_select != "single"
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13 mkdir reverse &&
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14 #end if
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16 #if $batch_cond.batch_select == "batch":
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17 #set elid = re.sub('[^\w\-\.]', '_', str($batch_cond.paired_cond.reads.element_identifier))
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18 #if $batch_cond.paired_cond.paired_select != "paired"
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19 ln -s '$batch_cond.paired_cond.reads' forward/'$elid' &&
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20 #else
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21 ln -s '$batch_cond.paired_cond.reads.forward' forward/'$elid' &&
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22 ln -s '$batch_cond.paired_cond.reads.reverse' reverse/'$elid' &&
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23 #end if
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24 #if $batch_cond.paired_cond.paired_select == "separate"
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25 ln -s '$batch_cond.paired_cond.sdaer' reverse/'$elid' &&
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26 #end if
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27 #else
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28 #for $read in $batch_cond.paired_cond.reads:
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29 #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
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30 #if $batch_cond.paired_cond.paired_select != "paired"
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31 ln -s '$read' forward/'$elid' &&
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32 #else
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33 ln -s '$read.forward' forward/'$elid' &&
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34 ln -s '$read.reverse' reverse/'$elid' &&
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35 #end if
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36 #end for
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37 #if $batch_cond.paired_cond.paired_select == "separate"
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38 #for $read in $batch_cond.paired_cond.sdaer:
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39 #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
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40 ln -s '$read' reverse/'$elid' &&
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41 #end for
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42 #end if
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43 #end if
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44
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45 Rscript --slave '$dada2_script'
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46 ]]></command>
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47 <configfiles>
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48 <configfile name="dada2_script"><![CDATA[
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49 #import re
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50 library(ggplot2, quietly=T)
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51 library(dada2, quietly=T)
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52
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53 #if $batch_cond.batch_select != "batch"
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54 agg = $batch_cond.aggregate
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55 #else
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56 agg = FALSE
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57 #end if
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58
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59 fwd_files = list.files("forward", full.names=T)
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60 qp <- plotQualityProfile(fwd_files, n=$n, aggregate = agg)
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61 ggsave('output.pdf', qp, width = 20,height = 15,units = c("cm"))
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62
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63 #if $batch_cond.paired_cond.paired_select != "single"
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64 rev_files = list.files("reverse", full.names=T)
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65 qp <- plotQualityProfile(rev_files, n=$n, aggregate = agg)
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66 ggsave('output_rev.pdf', qp, width = 20,height = 15,units = c("cm"))
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67 #end if
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68 ]]></configfile>
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69 </configfiles>
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70 <inputs>
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71 <conditional name="batch_cond">
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72 <param name="batch_select" type="select" label="Processing mode" help="Joint processing processes all reads at once in a single job creating a single output (two in the case of paired data). Batch processes the samples in separate jobs and creates separate output for each">
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73 <option value="joint">Joint</option>
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74 <option value="batch">Batch</option>
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75 </param>
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76 <when value="joint">
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77 <expand macro="fastq_input" multiple="True" collection_type="list:paired" argument_fwd="fl" argument_rev="fl"/>
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78 <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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79 </when>
9
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80 <when value="batch">
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81 <expand macro="fastq_input" multiple="False" collection_type="paired" argument_fwd="fl" argument_rev="fl"/>
3
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82 </when>
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83 </conditional>
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84 <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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85 </inputs>
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86 <outputs>
8
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87 <data name="output" format="pdf" from_work_dir="output.pdf">
9
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88 <filter>batch_cond['paired_cond']['paired_select'] == "single"</filter>
8
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89 </data>
9
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90 <data name="output_fwd" format="pdf" from_work_dir="output.pdf" label="${tool.name} on ${on_string}: forward reads">
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91 <filter>batch_cond['paired_cond']['paired_select'] != "single"</filter>
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92 </data>
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93 <data name="output_rev" format="pdf" from_work_dir="output_rev.pdf" label="${tool.name} on ${on_string}: reverse reads">
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94 <filter>batch_cond['paired_cond']['paired_select'] != "single"</filter>
8
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95 </data>
0
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96 </outputs>
2
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97 <tests>
9
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98 <!-- paired joint, no-aggregate -->
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99 <test expect_num_outputs="2">
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100 <param name="batch_cond|batch_select" value="joint"/>
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101 <param name="batch_cond|paired_cond|paired_select" value="paired"/>
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102 <param name="batch_cond|paired_cond|reads">
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103 <collection type="list:paired">
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104 <element name="F3D0_S188_L001">
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105 <collection type="paired">
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106 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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107 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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108 </collection>
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109 </element>
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110 </collection>
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111 </param>
9
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112 <param name="batch_cond|aggregate" value="FALSE"/>
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113 <output name="output_fwd" value="qualityProfileMultiple.pdf" ftype="pdf"/>
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114 <output name="output_rev" value="qualityProfileMultiple_rev.pdf" ftype="pdf"/>
2
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115 </test>
9
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116 <!-- paired-separate joint, no-aggregate (sim_size because element ids differ) -->
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117 <test expect_num_outputs="2">
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118 <param name="batch_cond|batch_select" value="joint"/>
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119 <param name="batch_cond|paired_cond|paired_select" value="separate"/>
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120 <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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121 <param name="batch_cond|paired_cond|sdaer" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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122 <param name="batch_cond|aggregate" value="FALSE"/>
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123 <output name="output_fwd" value="qualityProfileMultiple.pdf" ftype="pdf" compare="sim_size"/>
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124 <output name="output_rev" value="qualityProfileMultiple_rev.pdf" ftype="pdf" compare="sim_size"/>
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125 </test>
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126 <!-- single, non-batch, aggregate, small sample -->
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127 <test expect_num_outputs="1">
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128 <param name="batch_cond|batch_select" value="joint"/>
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129 <param name="batch_cond|paired_cond|paired_select" value="single"/>
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130 <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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131 <param name="n" value="10000"/>
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132 <param name="batch_cond|aggregate" value="TRUE"/>
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133 <output name="output" value="qualityProfileSmallSample.pdf" ftype="pdf"/>
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134 </test>
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135
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136 <!-- paired, batch -->
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137 <test expect_num_outputs="2">
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138 <param name="batch_cond|batch_select" value="batch"/>
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139 <param name="batch_cond|paired_cond|paired_select" value="paired"/>
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140 <param name="batch_cond|paired_cond|reads">
3
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141 <collection type="paired">
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142 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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143 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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144 </collection>
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145 </param>
8
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146 <output name="output_fwd" value="qualityProfile.pdf" ftype="pdf"/>
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147 <output name="output_rev" value="qualityProfile_rev.pdf" ftype="pdf"/>
2
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148 </test>
9
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149 <!-- paired-separate batch (sim_size because element ids differ)-->
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150 <test expect_num_outputs="2">
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151 <param name="batch_cond|batch_select" value="batch"/>
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152 <param name="batch_cond|paired_cond|paired_select" value="separate"/>
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153 <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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154 <param name="batch_cond|paired_cond|sdaer" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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155 <output name="output_fwd" value="qualityProfile.pdf" ftype="pdf" compare="sim_size"/>
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156 <output name="output_rev" value="qualityProfile_rev.pdf" ftype="pdf" compare="sim_size"/>
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157 </test>
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158 <!-- single, batch -->
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159 <test expect_num_outputs="1">
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160 <param name="batch_cond|batch_select" value="batch"/>
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161 <param name="batch_cond|paired_cond|paired_select" value="single"/>
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162 <param name="batch_cond|paired_cond|reads" 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>
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166 </tests>
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167 <help><![CDATA[
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168 Summary
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169 .......
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170
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171 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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172
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173 Details
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174 .......
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175
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176 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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177 to at least that position.
0
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178 ]]></help>
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179 <expand macro="citations"/>
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180 </tool>