Mercurial > repos > iuc > dada2_primercheck

annotate dada2_primercheck.xml @ 2:7dfcb39313d4 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 14:13:18 +0000
parents ee763baa80c3
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1 <tool id="dada2_primerCheck" name="dada2: primer check" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description></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="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 Rscript '$dada2_script'
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12 ]]></command>
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13 <configfiles>
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14 <configfile name="dada2_script"><![CDATA[
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15 #import re
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16 library(Biostrings, quietly=T)
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17 library(ShortRead, quietly=T)
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18
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19 FWD <- "$forward_primer"
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20 REV <- "$reverse_primer"
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21
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22 allOrients <- function(primer) {
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23 # Create all orientations of the input sequence
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24 dna <- DNAString(primer) # The Biostrings works w/ DNAString objects rather than character vectors
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25 orients <- c(Forward = dna, Complement = Biostrings::complement(dna), Reverse = Biostrings::reverse(dna), RevComp = Biostrings::reverseComplement(dna))
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26 return(sapply(orients, toString)) # Convert back to character vector
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27 }
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28 FWD.orients <- allOrients(FWD)
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29 REV.orients <- allOrients(REV)
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30
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31 primerHits <- function(primer, fn) {
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32 ## Counts number of reads in which the primer is found
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33 nhits <- vcountPattern(primer, sread(readFastq(fn)), fixed = FALSE)
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34 return(sum(nhits > 0))
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35 }
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36
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37 df <- NULL;
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38 #for $i, $read in enumerate($paired_cond.reads):
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39 #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
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40 #if $paired_cond.paired_select == "single"
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41 #set fwd_reads = $read
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42 #else
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43 #set fwd_reads = $read.forward
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44 #set rev_reads = $read.reverse
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45 #end if
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46 df <- rbind(df, c('$elid', 'FWD', 'FWD', sapply(FWD.orients, primerHits, fn = '$fwd_reads')))
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47 df <- rbind(df, c('$elid', 'REV', 'FWD', sapply(REV.orients, primerHits, fn = '$fwd_reads')))
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48 #if $paired_cond.paired_select != "single"
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49 df <- rbind(df, c('$elid', 'FWD', 'REV', sapply(FWD.orients, primerHits, fn = '$rev_reads')))
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50 df <- rbind(df, c('$elid', 'REV', 'REV', sapply(REV.orients, primerHits, fn = '$rev_reads')))
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51 #end if
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52 #end for
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53 colnames(df) <- c('Sample', 'Primer', 'ReadDir', 'Sequence', 'Complement', 'Reverse', 'RevComp')
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54 write.table(df, "$out", quote=F, sep="\t", row.names = F, col.names = T)
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55 ]]></configfile>
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56 </configfiles>
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57 <inputs>
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58 <expand macro="fastq_input" multiple="True" collection_type="list:paired" argument_fwd="fl" argument_rev="fl"/>
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59 <param name="forward_primer" type="text" label="Forward primer sequence">
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60 <validator type="empty_field" message="You need to specify a forward primer sequence"/>
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61 </param>
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62 <param name="reverse_primer" type="text" label="Reverse primer sequence">
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63 <validator type="empty_field" message="You need to specify a reverse primer sequence"/>
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64 </param>
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65 </inputs>
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66 <outputs>
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67 <data name="out" format="tabular"/>
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68 </outputs>
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69 <tests>
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70 <!-- paired data in paired collection -->
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71 <test expect_num_outputs="1">
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72 <conditional name="paired_cond">
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73 <param name="paired_select" value="paired"/>
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74 <param name="reads">
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75 <collection type="list:paired">
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76 <element name="F3D0_S188_L001">
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77 <collection type="paired">
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78 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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79 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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80 </collection>
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81 </element>
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82 <element name="F3D141_S207_L001">
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83 <collection type="paired">
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84 <element name="forward" value="F3D141_S207_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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85 <element name="reverse" value="F3D141_S207_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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86 </collection>
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87 </element>
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88 </collection>
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89 </param>
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90 </conditional>
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91
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92 <param name="forward_primer" value="ACCTGCGGARGGATCA"/>
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93 <param name="reverse_primer" value="GAGATCCRTTGYTRAAAGTT"/>
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94 <output name="out">
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95 <assert_contents>
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96 <has_n_lines n="9"/>
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97 <has_n_columns n="7"/>
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98 </assert_contents>
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99 </output>
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100 </test>
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101 <!-- single end data -->
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102 <test expect_num_outputs="1">
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103 <conditional name="paired_cond">
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104 <param name="paired_select" value="single"/>
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105 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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106 </conditional>
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107 <param name="forward_primer" value="ACCTGCGGARGGATCA"/>
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108 <param name="reverse_primer" value="GAGATCCRTTGYTRAAAGTT"/>
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109 <output name="out">
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110 <assert_contents>
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111 <has_n_lines n="3"/>
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112 <has_n_columns n="7"/>
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113 </assert_contents>
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114 </output>
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115 </test>
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116 </tests>
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117
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118 <help><![CDATA[
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119 Description
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120 ...........
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121
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122 Simple check for primer sequences in sequencing data. The tool counts the number
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123 of occurrences of the primer sequence, its complement, the reverse and the
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124 reverse complement.
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125
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126 See also: https://benjjneb.github.io/dada2/ITS_workflow.html#identify-primers
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127
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128 Usage
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129 .....
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130
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131 **Input** FASTQ datasets and forward and reverse primers
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132
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133 **Output** a table listing the counts of the different occurrences in the read files.
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134
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135
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136 @HELP_OVERVIEW@
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137 ]]></help>
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138 <expand macro="citations"/>
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139 </tool>