Mercurial > repos > matthias > dada2_plotqualityprofile

annotate dada2_plotQualityProfile.xml @ 2:4095456821e2 draft

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author matthias
date Tue, 09 Apr 2019 07:03:51 -0400
parents de5c51e1c190
children cf166b8a8e27
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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 Rscript --slave '$dada2_script'
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10 ]]></command>
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11 <configfiles>
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12 <configfile name="dada2_script"><![CDATA[
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13 files = c()
2
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14 #if "batch" in $paired_cond.paired_select
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15 #if "single" in $paired_cond.paired_select
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16 files = c(files, '$reads')
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17 #else
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18 files = c(files, '$reads.forward')
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19 files = c(files, '$reads.reverse')
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20 #end if
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21 #else
2
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22 #for $read in $paired_cond.reads:
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23 #if $paired_cond.paired_select == "no"
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24 files = c(files, '$read')
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25 #else
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26 files = c(files, '$read.forward')
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27 files = c(files, '$read.reverse')
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28 #end if
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29 #end for
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30 #end if
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31
2
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32
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33 library(ggplot2, quietly=T)
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34 library(dada2, quietly=T)
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35
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36 qp <- plotQualityProfile(files,
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37 #if str($n) != ""
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38 n=$n,
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39 #end if
2
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40 aggregate = $mode)
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41
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42 ggsave('output.pdf', qp, width = 20,height = 15,units = c("cm"))
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43 ]]></configfile>
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44 </configfiles>
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45 <inputs>
2
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46 <conditional name="paired_cond">
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47 <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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48 <option value="paired">paired - non batch</option>
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49 <option value="single">single - non batch</option>
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50 <option value="paired_batch">paired - batch</option>
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51 <option value="single_batch">single - batch</option>
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52 </param>
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53 <when value="paired">
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54 <param name="reads" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
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55 </when>
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56 <when value="single">
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57 <param name="reads" type="data" multiple="true" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
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58 </when>
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59 <when value="paired_batch">
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60 <param name="reads" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
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61 </when>
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62 <when value="single_batch">
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63 <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
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64 </when>
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65 </conditional>
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66 <param name="mode" 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"/>
0
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67 <param name="n" type="integer" optional="true" label="sample number" help="number of records to sample from the fastq file (default 500.000)"/>
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68 </inputs>
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69 <outputs>
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70 <data name="output" format="pdf" from_work_dir="output.pdf"/>
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71 </outputs>
2
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72 <tests>
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73 <test>
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74 <param name="mode" value="TRUE"/>
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75 <conditional name="paired_cond">
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76 <param name="paired_select" value="TRUE"/>
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77 <param name="reads">
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78 <collection type="paired">
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79 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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80 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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81 </collection>
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82 </param>
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83 </conditional>
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84 <output name="output" value="qualityProfileMultiple.pdf" ftype="pdf"/>
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85 </test>
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86 <test>
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87 <param name="mode" value="FALSE"/>
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88 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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89 <output name="output" value="qualityProfile.pdf" ftype="pdf"/>
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90 </test>
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91 <test>
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92 <param name="mode" value="FALSE"/>
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93 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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94 <param name="n" value="10000"/>
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95 <output name="output" value="qualityProfileSmallSample.pdf" ftype="pdf"/>
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96 </test>
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97 </tests>
0
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98 <help><![CDATA[
2
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99 Summary
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100 .......
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101
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102 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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103
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104 Details
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105 .......
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106
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107 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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108 to at least that position.
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109
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110 Note this tool ignores the pairing of the reads, but the data is just processed as list.
0
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111 ]]></help>
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112 <expand macro="citations"/>
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113 </tool>