Mercurial > repos > iuc > dada2_plotcomplexity

annotate dada2_plotComplexity.xml @ 5:8daf4564ccda draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 28506788978bf5f0ce31dca09b7ca3d6d4900edb"
author iuc
date Fri, 02 Jul 2021 20:09:37 +0000
parents 1728e5ee871a
children 555ccac8a4c5
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ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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1 <tool id="dada2_plotComplexity" name="dada2: plotComplexity" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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2 <description>Plot sequence complexity profile</description>
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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3 <macros>
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4 <import>macros.xml</import>
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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5 </macros>
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6 <expand macro="requirements"/>
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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9 <command detect_errors="exit_code"><![CDATA[
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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10 ##name files by linking
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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11 #import re
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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12 mkdir forward &&
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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13 #if $batch_cond.paired_cond.paired_select != "single"
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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14 mkdir reverse &&
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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15 #end if
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16
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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17 #if $batch_cond.batch_select == "batch":
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18 #set elid = re.sub('[^\w\-\.]', '_', str($batch_cond.paired_cond.reads.element_identifier))
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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19 #if $batch_cond.paired_cond.paired_select != "paired"
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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20 ln -s '$batch_cond.paired_cond.reads' forward/'$elid' &&
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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21 #else
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22 ln -s '$batch_cond.paired_cond.reads.forward' forward/'$elid' &&
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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23 ln -s '$batch_cond.paired_cond.reads.reverse' reverse/'$elid' &&
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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24 #end if
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25 #if $batch_cond.paired_cond.paired_select == "separate"
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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26 ln -s '$batch_cond.paired_cond.sdaer' reverse/'$elid' &&
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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27 #end if
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28 #else
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29 #for $read in $batch_cond.paired_cond.reads:
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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30 #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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31 #if $batch_cond.paired_cond.paired_select != "paired"
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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32 ln -s '$read' forward/'$elid' &&
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33 #else
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34 ln -s '$read.forward' forward/'$elid' &&
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35 ln -s '$read.reverse' reverse/'$elid' &&
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36 #end if
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37 #end for
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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38 #if $batch_cond.paired_cond.paired_select == "separate"
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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39 #for $read in $batch_cond.paired_cond.sdaer:
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40 #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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41 ln -s '$read' reverse/'$elid' &&
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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42 #end for
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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43 #end if
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44 #end if
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45
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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46 Rscript --slave '$dada2_script'
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47 ]]></command>
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48 <configfiles>
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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49 <configfile name="dada2_script"><![CDATA[
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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50 #import re
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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51 library(ggplot2, quietly=T)
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52 library(dada2, quietly=T)
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53
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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54 #if $batch_cond.batch_select != "batch"
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55 agg <- $batch_cond.aggregate
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56 #else
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57 agg <- FALSE
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58 #end if
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59
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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60 #if str($window) == ""
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61 wndw <- NULL
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62 #else
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63 wndw <- $window
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64 #end if
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65
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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66 fwd_files <- list.files("forward", full.names=T)
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67 qp <- plotComplexity(fwd_files, kmerSize=$kmerSize, window=wndw, by=$by, n=$n, bins=$bins, aggregate = agg)
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68 ggsave('output.pdf', qp, width = 20,height = 15,units = c("cm"))
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69
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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70 #if $batch_cond.paired_cond.paired_select != "single"
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71 rev_files <- list.files("reverse", full.names=T)
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72 qp <- plotComplexity(rev_files, kmerSize=$kmerSize, window=wndw, by=$by, n=$n, bins=$bins, aggregate = agg)
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73 ggsave('output_rev.pdf', qp, width = 20,height = 15,units = c("cm"))
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74 #end if
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75 ]]></configfile>
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76 </configfiles>
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77 <inputs>
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78 <conditional name="batch_cond">
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79 <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">
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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80 <option value="joint">Joint</option>
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81 <option value="batch">Batch</option>
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82 </param>
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83 <when value="joint">
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84 <expand macro="fastq_input" multiple="True" collection_type="list:paired" argument_fwd="fl" argument_rev="fl"/>
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85 <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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86 </when>
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87 <when value="batch">
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88 <expand macro="fastq_input" multiple="False" collection_type="paired" argument_fwd="fl" argument_rev="fl"/>
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89 </when>
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90 </conditional>
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91 <param argument="kmerSize" type="integer" value="2" label="kmer size" help="kmer: also known as oligonucleotides words"/>
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92 <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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93 <param argument="by" type="integer" value="5" label="step size (nucleotides)" help="between each moving window tested"/>
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94 <param argument="n" type="integer" value="100000" label="sample number" help="number of records to sample from the fastq file"/>
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95 <param argument="bins" type="integer" value="100" label="number of bins to use for the histogram" help=""/>
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96 </inputs>
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97 <outputs>
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98 <data name="output" format="pdf" from_work_dir="output.pdf">
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99 <filter>batch_cond['paired_cond']['paired_select'] == "single"</filter>
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100 </data>
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101 <data name="output_fwd" format="pdf" from_work_dir="output.pdf" label="${tool.name} on ${on_string}: forward reads">
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102 <filter>batch_cond['paired_cond']['paired_select'] != "single"</filter>
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103 </data>
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104 <data name="output_rev" format="pdf" from_work_dir="output_rev.pdf" label="${tool.name} on ${on_string}: reverse reads">
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105 <filter>batch_cond['paired_cond']['paired_select'] != "single"</filter>
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106 </data>
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107 </outputs>
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108 <tests>
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109 <!-- all tests are against the same file using a delta that should ensure that the pdf contains a plot -->
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110 <!-- paired joint, no-aggregate -->
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111 <test expect_num_outputs="2">
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112 <param name="batch_cond|batch_select" value="joint"/>
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113 <param name="batch_cond|paired_cond|paired_select" value="paired"/>
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114 <param name="batch_cond|paired_cond|reads">
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115 <collection type="list:paired">
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116 <element name="F3D0_S188_L001">
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117 <collection type="paired">
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118 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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119 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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120 </collection>
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121 </element>
2
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parents: 0
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122 <element name="F3D141_S207_L001">
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123 <collection type="paired">
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parents: 0
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124 <element name="forward" value="F3D141_S207_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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parents: 0
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125 <element name="reverse" value="F3D141_S207_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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126 </collection>
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127 </element>
0
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128 </collection>
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129 </param>
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130 <param name="batch_cond|aggregate" value="FALSE"/>
2
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131 <output name="output_fwd" value="complexity_fwd.pdf" ftype="pdf" compare="sim_size" delta="200"/>
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132 <output name="output_rev" value="complexity_rev.pdf" ftype="pdf" compare="sim_size" delta="200"/>
0
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133 </test>
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134 <!-- paired-separate joint, no-aggregate (sim_size because element ids differ) -->
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135 <test expect_num_outputs="2">
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136 <param name="batch_cond|batch_select" value="joint"/>
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parents:
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137 <param name="batch_cond|paired_cond|paired_select" value="separate"/>
2
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parents: 0
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138 <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D141_S207_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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parents: 0
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139 <param name="batch_cond|paired_cond|sdaer" value="F3D0_S188_L001_R2_001.fastq.gz,F3D141_S207_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
0
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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140 <param name="batch_cond|aggregate" value="FALSE"/>
2
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141 <output name="output_fwd" value="complexity_fwd.pdf" ftype="pdf" compare="sim_size" delta="200"/>
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parents: 0
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142 <output name="output_rev" value="complexity_rev.pdf" ftype="pdf" compare="sim_size" delta="200"/>
0
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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143 </test>
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144 <!-- single, non-batch, aggregate, small sample -->
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145 <test expect_num_outputs="1">
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146 <param name="batch_cond|batch_select" value="joint"/>
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147 <param name="batch_cond|paired_cond|paired_select" value="single"/>
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148 <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"/>
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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149 <param name="n" value="10000"/>
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150 <param name="batch_cond|aggregate" value="TRUE"/>
2
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151 <output name="output" value="complexity_fwd.pdf" ftype="pdf" compare="sim_size" delta="900"/>
0
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152 </test>
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153
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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parents:
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154 <!-- paired, batch -->
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155 <test expect_num_outputs="2">
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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parents:
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156 <param name="batch_cond|batch_select" value="batch"/>
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parents:
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157 <param name="batch_cond|paired_cond|paired_select" value="paired"/>
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158 <param name="batch_cond|paired_cond|reads">
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159 <collection type="paired">
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parents:
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160 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
ab2030f217a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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parents:
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161 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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162 </collection>
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163 </param>
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164 <output name="output_fwd" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/>
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165 <output name="output_rev" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/>
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166 </test>
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167 <!-- paired-separate batch (sim_size because element ids differ)-->
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168 <test expect_num_outputs="2">
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169 <param name="batch_cond|batch_select" value="batch"/>
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170 <param name="batch_cond|paired_cond|paired_select" value="separate"/>
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171 <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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172 <param name="batch_cond|paired_cond|sdaer" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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173 <output name="output_fwd" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/>
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174 <output name="output_rev" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/>
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175 </test>
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176 <!-- single, batch -->
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177 <test expect_num_outputs="1">
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178 <param name="batch_cond|batch_select" value="batch"/>
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179 <param name="batch_cond|paired_cond|paired_select" value="single"/>
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180 <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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181 <param name="n" value="10000"/>
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182 <output name="output" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/>
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183 </test>
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184 </tests>
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185 <help><![CDATA[
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186 Summary
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187 .......
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188
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189 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).
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190
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191 Details
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192 .......
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193
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194 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.
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195
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196
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197 @HELP_OVERVIEW@
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198 ]]></help>
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199 <expand macro="citations"/>
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200 </tool>