Mercurial > repos > iuc > dada2_removebimeradenovo

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 3dd3145db6ed58efc3bf5f71e96515173967fc72
author iuc
date Sat, 07 Dec 2024 08:47:32 +0000
parents 7136e9ab70db
children
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1 <tool id="dada2_removeBimeraDenovo" name="dada2: removeBimeraDenovo" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">
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2 <description>Remove bimeras from collections of unique sequences</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
6
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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 library(dada2, quietly=T)
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16 @READ_FOO@
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17 @WRITE_FOO@
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19 unqs <- $read_data($unqs)
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21 seqtab.nochim <- removeBimeraDenovo(unqs, method = "$method")
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22
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23 ## - output is data.frame (mergepairs) or sequencetable (if this was the input)
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24 ## in the former case the (multi item) list is stored as RDS
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25 ## in the latter case the named int matrix is stored as tabular (rows=samples, columns=ASVs)
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26 ## - otherwise uniques-vector, i.e. a named integer vector
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27
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28 #if $unqs.is_of_type('dada2_dada')
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29 write.data( seqtab.nochim, '$stable_uniques', "dada2_uniques" )
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30 #else if $unqs.is_of_type('dada2_sequencetable')
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31 write.data( seqtab.nochim, '$stable_sequencetable', "dada2_sequencetable" )
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32 #else if $unqs.is_of_type('dada2_mergepairs')
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33 write.data( seqtab.nochim, '$stable_mergepairs', "dada2_mergepairs" )
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34 #end if
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35
7
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36 cat("remaining nonchimeric: ", 100*sum(getUniques(seqtab.nochim))/sum(getUniques(unqs)), "%")
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37 ]]></configfile>
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38 </configfiles>
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39 <inputs>
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40 <param name="unqs" type="data" format="@DADA_UNIQUES@,dada2_sequencetable" label="sequence table" help=""/>
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41 <param argument="method" type="select" label="Method">
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42 <option value="consensus">check samples independently for bimeras and make a consensus decision on each sequence variant</option>
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43 <option value="pooled">pool samples for bimera identification</option>
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44 <option value="per-sample">check samples independently for bimeras and remove (0-out) sequence variants from samples independently</option>
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45 </param>
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46 </inputs>
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47 <outputs>
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48 <!-- fix output filters in a later release https://github.com/galaxyproject/galaxy/issues/7464 -->
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49 <data name="stable_uniques" format="dada2_uniques" label="${tool.name} on ${on_string}" from_work_dir="nonchim.uniques">
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50 <filter>unqs.ext == "dada2_dada"</filter>
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51 </data>
6
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52 <data name="stable_mergepairs" format="dada2_mergepairs" label="${tool.name} on ${on_string}: mergePairs" from_work_dir="nonchim.mergepairs">
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53 <filter>unqs.ext == "dada2_mergepairs"</filter>
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54 </data>
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55 <data name="stable_sequencetable" format="dada2_sequencetable" label="${tool.name} on ${on_string}: sequencetable" from_work_dir="nonchim.mergepairs">
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56 <filter>unqs.ext == "dada2_sequencetable"</filter>
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57 </data>
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58 </outputs>
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59 <tests>
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60 <test expect_num_outputs="1">
2
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61 <param name="unqs" ftype="dada2_sequencetable" value="makeSequenceTable.tab"/>
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62 <output name="stable_sequencetable" value="removeBimeraDenovo.tab" ftype="dada2_sequencetable" />
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63 </test>
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64 <!-- dada input -->
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65 <test expect_num_outputs="1">
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66 <param name="unqs" ftype="dada2_dada" value="dada_F3D0_S188_L001_R1.Rdata"/>
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67 <output name="stable_uniques" value="removeBimeraDenovo_F3D0_dada_uniques.tab" ftype="dada2_uniques" />
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68 </test>
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69 <!-- mergepairs input + non default-->
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70 <test expect_num_outputs="1">
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71 <param name="unqs" ftype="dada2_mergepairs" value="mergePairs_F3D0_S188_L001.Rdata"/>
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72 <param name="method" value="pooled"/>
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73 <output name="stable_mergepairs" value="removeBimeraDenovo_F3D0_mergepairs.Rdata" ftype="dada2_mergepairs" compare="sim_size" delta="400"/>
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74 </test>
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75 </tests>
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76 <help><![CDATA[
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77 Description
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78 ...........
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79
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80 This tool can be used to remove chimeric sequences, i.e. sequences that can be constructed by combining a left-segment and a right-segment from two more abundant “parent” sequences.. Two methods to identify chimeras are supported: Identification from pooled sequences and identification by consensus across samples.
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81
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82 - from **pooled** sequences: Each sequence is evaluated against a set of "parents" drawn from the sequence collection that are sufficiently more abundant than the sequence being evaluated. Sequences that are bimera are removed, i.e. a two-parent chimera, in which the left side is made up of one parent sequence, and the right-side made up of a second parent sequence.
1937c2b4da7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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83 - by **consensus**: In short, bimeric sequences are flagged on a sample-by-sample basis. Then, a vote is performed for each sequence across all samples in which it appeared. If the sequence is flagged in a sufficiently high fraction of samples, it is identified as a bimera. A logical vector is returned, with an entry for each sequence in the table indicating whether it was identified as bimeric by this consensus procedure.
1937c2b4da7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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84
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85 Usage
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86 .....
1937c2b4da7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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87
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88 **Input**
1937c2b4da7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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89
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90 - the results of makeSequenceTable (note that also the results of dada, and mergePairs are accepted)
1937c2b4da7a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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91
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92 **Output**
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93
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94 A data set of type:
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95 - dada2_sequenceTable (resp. dada2_mergepairs) if the input is of type dada2_sequenceTable (resp. dada2_mergepairs)
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96 - dada2_uniques otherwise
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97
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98 Details
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99 .......
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100
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101 The frequency of chimeric sequences varies substantially from dataset to dataset, and depends on on factors including experimental procedures and sample complexity. Here chimeras make up about 21% of the merged sequence variants, but when we account for the abundances of those variants we see they account for only about 4% of the merged sequence reads.
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102
10
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103 Considerations for your own data: Most of your reads should remain after chimera removal (it is not uncommon for a majority of sequence variants to be removed though). If most of your reads were removed as chimeric, upstream processing may need to be revisited.
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104 In almost all cases this is caused by primer sequences with ambiguous nucleotides that were not removed prior to beginning the DADA2 pipeline.
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105 You can check for present primer sequences with the tool `dada2: primer check`
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106
0
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107
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108 @HELP_OVERVIEW@
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109 ]]></help>
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110 <expand macro="citations"/>
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111 </tool>