Mercurial > repos > iuc > dada2_plotqualityprofile

annotate dada2_plotQualityProfile.xml @ 11:e7c2674e01fe draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 commit f65944aa0547c2fbe4b746cf443c85b2a76e9a48
author iuc
date Sat, 20 Dec 2025 14:17:50 +0000
parents 4e469b758915
children
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4e469b758915 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit bbbc0e71b1db299a7c7296f25ac7adcccd27fbe3
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1 <tool id="dada2_plotQualityProfile" name="dada2: plotQualityProfile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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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>
6
a58e4a43f49c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <expand macro="version_command"/>
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10 <command detect_errors="exit_code"><![CDATA[
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11 ##name files by linking
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12 #import re
371afe17d247 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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13 mkdir forward &&
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14 #if $batch_cond.paired_cond.paired_select != "single"
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15 mkdir reverse &&
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16 #end if
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17
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18 #if $batch_cond.batch_select == "batch":
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19 #set elid = re.sub('[^\w\-\.]', '_', str($batch_cond.paired_cond.reads.element_identifier))
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20 #if $batch_cond.paired_cond.paired_select != "paired"
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21 ln -s '$batch_cond.paired_cond.reads' forward/'$elid' &&
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22 #else
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23 ln -s '$batch_cond.paired_cond.reads.forward' forward/'$elid' &&
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24 ln -s '$batch_cond.paired_cond.reads.reverse' reverse/'$elid' &&
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25 #end if
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26 #else
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27 #for $read in $batch_cond.paired_cond.reads:
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28 #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
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29 #if $batch_cond.paired_cond.paired_select != "paired"
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30 ln -s '$read' forward/'$elid' &&
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31 #else
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32 ln -s '$read.forward' forward/'$elid' &&
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33 ln -s '$read.reverse' reverse/'$elid' &&
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34 #end if
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35 #end for
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36 #end if
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37
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38 Rscript --slave '$dada2_script'
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39 ]]></command>
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40 <configfiles>
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41 <configfile name="dada2_script"><![CDATA[
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42 #import re
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43 library(ggplot2, quietly=T)
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44 library(dada2, quietly=T)
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45
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46 #if $batch_cond.batch_select != "batch"
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47 agg = $batch_cond.aggregate
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48 #else
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49 agg = FALSE
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50 #end if
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51
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52 fwd_files = list.files("forward", full.names=T)
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53 qp <- plotQualityProfile(fwd_files, n=$n, aggregate = agg)
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54 ggsave('output.pdf', qp, width = 20,height = 15,units = c("cm"))
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55
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56 #if $batch_cond.paired_cond.paired_select != "single"
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57 rev_files = list.files("reverse", full.names=T)
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58 qp <- plotQualityProfile(rev_files, n=$n, aggregate = agg)
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59 ggsave('output_rev.pdf', qp, width = 20,height = 15,units = c("cm"))
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60 #end if
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61 ]]></configfile>
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62 </configfiles>
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63 <inputs>
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64 <conditional name="batch_cond">
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65 <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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66 <option value="joint">Joint</option>
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67 <option value="batch">Batch</option>
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68 </param>
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69 <when value="joint">
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70 <expand macro="fastq_input" multiple="True" collection_type="list:paired" argument_fwd="fl" argument_rev="fl"/>
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71 <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"/>
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72 </when>
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73 <when value="batch">
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74 <expand macro="fastq_input" multiple="False" collection_type="paired" argument_fwd="fl" argument_rev="fl"/>
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75 </when>
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76 </conditional>
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77 <param argument="n" type="integer" value="500000" label="sample number" help="number of records to sample from the fastq file"/>
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78 </inputs>
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79 <outputs>
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80 <data name="output" format="pdf" from_work_dir="output.pdf">
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81 <filter>batch_cond['paired_cond']['paired_select'] == "single"</filter>
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82 </data>
8
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83 <data name="output_fwd" format="pdf" default_identifier_source="batch_cond|paired_cond|reads" from_work_dir="output.pdf" label="${tool.name} on ${on_string}: forward reads">
0
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84 <filter>batch_cond['paired_cond']['paired_select'] != "single"</filter>
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85 </data>
8
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86 <data name="output_rev" format="pdf" default_identifier_source="batch_cond|paired_cond|sdaer" from_work_dir="output_rev.pdf" label="${tool.name} on ${on_string}: reverse reads">
0
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87 <filter>batch_cond['paired_cond']['paired_select'] != "single"</filter>
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88 </data>
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89 </outputs>
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90 <tests>
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91 <!-- all tests are against the same file using a delta that should ensure that the pdf contains a plot -->
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92 <!-- paired joint, no-aggregate -->
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93 <test expect_num_outputs="2">
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94 <param name="batch_cond|batch_select" value="joint"/>
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95 <param name="batch_cond|paired_cond|paired_select" value="paired"/>
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96 <param name="batch_cond|paired_cond|reads">
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97 <collection type="list:paired">
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98 <element name="F3D0_S188_L001">
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99 <collection type="paired">
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100 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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101 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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102 </collection>
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103 </element>
2
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104 <element name="F3D141_S207_L001">
2a90d2fd3336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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105 <collection type="paired">
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106 <element name="forward" value="F3D141_S207_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
2a90d2fd3336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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107 <element name="reverse" value="F3D141_S207_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
2a90d2fd3336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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108 </collection>
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109 </element>
0
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110 </collection>
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111 </param>
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112 <param name="batch_cond|aggregate" value="FALSE"/>
2
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113 <output name="output_fwd" value="qualityProfile_fwd.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
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114 <output name="output_rev" value="qualityProfile_rev.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
0
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115 </test>
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116 <!-- single, non-batch, aggregate, small sample -->
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117 <test expect_num_outputs="1">
371afe17d247 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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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="single"/>
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120 <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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121 <param name="n" value="10000"/>
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122 <param name="batch_cond|aggregate" value="TRUE"/>
2
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123 <output name="output" value="qualityProfile_fwd.pdf" ftype="pdf" compare="sim_size" delta="16000"/>
0
371afe17d247 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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124 </test>
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125
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126 <!-- paired, batch -->
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127 <test expect_num_outputs="2">
371afe17d247 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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128 <param name="batch_cond|batch_select" value="batch"/>
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129 <param name="batch_cond|paired_cond|paired_select" value="paired"/>
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130 <param name="batch_cond|paired_cond|reads">
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131 <collection type="paired">
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132 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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133 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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134 </collection>
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135 </param>
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136 <output name="output_fwd" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
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137 <output name="output_rev" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
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138 </test>
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139 <!-- single, batch -->
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140 <test expect_num_outputs="1">
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141 <param name="batch_cond|batch_select" value="batch"/>
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142 <param name="batch_cond|paired_cond|paired_select" value="single"/>
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143 <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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144 <param name="n" value="10000"/>
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145 <output name="output" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
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146 </test>
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147 </tests>
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148 <help><![CDATA[
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149 Summary
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150 .......
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151
371afe17d247 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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152 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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153
371afe17d247 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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154 Details
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155 .......
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156
371afe17d247 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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157 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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158 to at least that position.
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159
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160 @HELP_OVERVIEW@
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161 ]]></help>
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162 <expand macro="citations"/>
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163 </tool>