Mercurial > repos > iuc > dada2_plotcomplexity

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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 14:10:33 +0000
parents 69491e90c0f3
children
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69491e90c0f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit bbbc0e71b1db299a7c7296f25ac7adcccd27fbe3
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1 <tool id="dada2_plotComplexity" name="dada2: plotComplexity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
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2 <description>Plot sequence complexity profile</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
6
9a88f458440d 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
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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 <- $batch_cond.aggregate
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48 #else
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49 agg <- FALSE
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50 #end if
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51
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52 #if str($window) == ""
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53 wndw <- NULL
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54 #else
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55 wndw <- $window
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56 #end if
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57
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58 fwd_files <- list.files("forward", full.names=T)
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59 qp <- plotComplexity(fwd_files, kmerSize=$kmerSize, window=wndw, by=$by, n=$n, bins=$bins, aggregate = agg)
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60 ggsave('output.pdf', qp, width = 20,height = 15,units = c("cm"))
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61
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62 #if $batch_cond.paired_cond.paired_select != "single"
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63 rev_files <- list.files("reverse", full.names=T)
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64 qp <- plotComplexity(rev_files, kmerSize=$kmerSize, window=wndw, by=$by, n=$n, bins=$bins, aggregate = agg)
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65 ggsave('output_rev.pdf', qp, width = 20,height = 15,units = c("cm"))
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66 #end if
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67 ]]></configfile>
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68 </configfiles>
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69 <inputs>
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70 <conditional name="batch_cond">
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71 <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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72 <option value="joint">Joint</option>
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73 <option value="batch">Batch</option>
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74 </param>
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75 <when value="joint">
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76 <expand macro="fastq_input" multiple="True" collection_type="list:paired" argument_fwd="fl" argument_rev="fl"/>
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77 <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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78 </when>
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79 <when value="batch">
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80 <expand macro="fastq_input" multiple="False" collection_type="paired" argument_fwd="fl" argument_rev="fl"/>
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81 </when>
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82 </conditional>
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83 <param argument="kmerSize" type="integer" value="2" label="kmer size" help="kmer: also known as oligonucleotides words"/>
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84 <param argument="window" type="integer" value="" optional="true" label="width (nucleotides) of the moving window" help="If not specified (default) the whole sequence is used"/>
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85 <param argument="by" type="integer" value="5" label="step size (nucleotides)" help="between each moving window tested"/>
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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86 <param argument="n" type="integer" value="100000" label="sample number" help="number of records to sample from the fastq file"/>
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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87 <param argument="bins" type="integer" value="100" label="number of bins to use for the histogram" help=""/>
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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88 </inputs>
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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89 <outputs>
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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90 <data name="output" format="pdf" from_work_dir="output.pdf">
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91 <filter>batch_cond['paired_cond']['paired_select'] == "single"</filter>
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92 </data>
8
e7f76f1abf3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 3dd3145db6ed58efc3bf5f71e96515173967fc72
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93 <data name="output_fwd" format="pdf" default_identifier_source="batch_cond|paired_cond|reads" from_work_dir="output.pdf" label="${tool.name} on ${on_string}: forward reads">
0
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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94 <filter>batch_cond['paired_cond']['paired_select'] != "single"</filter>
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95 </data>
8
e7f76f1abf3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 3dd3145db6ed58efc3bf5f71e96515173967fc72
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96 <data name="output_rev" format="pdf" default_identifier_source="batch_cond|paired_cond|sdaer" from_work_dir="output_rev.pdf" label="${tool.name} on ${on_string}: reverse reads">
0
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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97 <filter>batch_cond['paired_cond']['paired_select'] != "single"</filter>
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98 </data>
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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99 </outputs>
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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100 <tests>
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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101 <!-- all tests are against the same file using a delta that should ensure that the pdf contains a plot -->
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102 <!-- paired joint, no-aggregate -->
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103 <test expect_num_outputs="2">
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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104 <param name="batch_cond|batch_select" value="joint"/>
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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105 <param name="batch_cond|paired_cond|paired_select" value="paired"/>
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106 <param name="batch_cond|paired_cond|reads">
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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107 <collection type="list:paired">
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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108 <element name="F3D0_S188_L001">
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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109 <collection type="paired">
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110 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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111 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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112 </collection>
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113 </element>
2
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114 <element name="F3D141_S207_L001">
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115 <collection type="paired">
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116 <element name="forward" value="F3D141_S207_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
10cd92444a38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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117 <element name="reverse" value="F3D141_S207_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
10cd92444a38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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118 </collection>
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119 </element>
0
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120 </collection>
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121 </param>
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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122 <param name="batch_cond|aggregate" value="FALSE"/>
2
10cd92444a38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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123 <output name="output_fwd" value="complexity_fwd.pdf" ftype="pdf" compare="sim_size" delta="200"/>
10cd92444a38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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124 <output name="output_rev" value="complexity_rev.pdf" ftype="pdf" compare="sim_size" delta="200"/>
0
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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125 </test>
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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126 <!-- single, non-batch, aggregate, small sample -->
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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127 <test expect_num_outputs="1">
923d45f161cf "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="joint"/>
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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129 <param name="batch_cond|paired_cond|paired_select" value="single"/>
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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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"/>
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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131 <param name="n" value="10000"/>
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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132 <param name="batch_cond|aggregate" value="TRUE"/>
2
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133 <output name="output" value="complexity_fwd.pdf" ftype="pdf" compare="sim_size" delta="900"/>
0
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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134 </test>
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135
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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136 <!-- paired, batch -->
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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137 <test expect_num_outputs="2">
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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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">
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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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"/>
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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143 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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144 </collection>
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145 </param>
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146 <output name="output_fwd" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/>
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147 <output name="output_rev" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/>
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148 </test>
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149 <!-- single, batch -->
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150 <test expect_num_outputs="1">
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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="single"/>
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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="n" value="10000"/>
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155 <output name="output" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/>
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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156 </test>
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157 </tests>
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158 <help><![CDATA[
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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159 Summary
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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160 .......
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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161
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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162 This function plots a histogram of the distribution of sequence complexities in the form of effective numbers of kmers as determined by seqComplexity. By default, kmers of size 2 are used, in which case a perfectly random sequences will approach an effective kmer number of 16 = 4 (nucleotides)^ 2 (kmer size).
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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163
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164 Details
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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165 .......
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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166
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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167 This function calculates the kmer complexity of input sequences. Complexity is quantified as the Shannon richness of kmers, which can be thought of as the effective number of kmers if they were all at equal frequencies. If a window size is provided, the minimum Shannon richness observed over sliding window along the sequence is returned.
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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168
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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169
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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170 @HELP_OVERVIEW@
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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171 ]]></help>
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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172 <expand macro="citations"/>
923d45f161cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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173 </tool>