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1 <?xml version="1.0" ?>
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2 <tool id="qiime_quality-control_filter-reads" name="qiime quality-control filter-reads"
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3 version="2020.8">
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4 <description>Filter demultiplexed sequences by alignment to reference database.</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime quality-control filter-reads
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10
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11 --i-demultiplexed-sequences=$idemultiplexedsequences
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12
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13 --i-database=$idatabase
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14
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15 --p-n-threads=$pnthreads
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16
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17 #if str($pmode) != 'None':
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18 --p-mode=$pmode
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19 #end if
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20
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21 #if str($psensitivity) != 'None':
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22 --p-sensitivity=$psensitivity
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23 #end if
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24
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25 --p-ref-gap-open-penalty=$prefgapopenpenalty
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26
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27 --p-ref-gap-ext-penalty=$prefgapextpenalty
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28
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29 #if $pnoexcludeseqs:
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30 --p-no-exclude-seqs
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31 #end if
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32
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33 --o-filtered-sequences=ofilteredsequences
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34
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35 #if str($examples) != 'None':
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36 --examples=$examples
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37 #end if
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38
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39 ;
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40 cp ofilteredsequences.qza $ofilteredsequences
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41
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42 ]]></command>
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43 <inputs>
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44 <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality²] The sequences to be trimmed. [required]" name="idemultiplexedsequences" optional="False" type="data" />
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45 <param format="qza,no_unzip.zip" label="--i-database: ARTIFACT Bowtie2 indexed database. Bowtie2Index [required]" name="idatabase" optional="False" type="data" />
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46 <param label="--p-mode: " name="pmode" optional="True" type="select">
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47 <option selected="True" value="None">Selection is Optional</option>
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48 <option value="local">local</option>
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49 <option value="global">global</option>
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50 </param>
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51 <param label="--p-sensitivity: " name="psensitivity" optional="True" type="select">
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52 <option selected="True" value="None">Selection is Optional</option>
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53 <option value="very-fast">very-fast</option>
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54 <option value="fast">fast</option>
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55 <option value="sensitive">sensitive</option>
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56 <option value="very-sensitive">very-sensitive</option>
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57 </param>
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58 <param label="--p-ref-gap-open-penalty: INTEGER Range(1, None) Reference gap open penalty. [default: 5]" min="1" name="prefgapopenpenalty" optional="True" type="integer" value="5" />
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59 <param label="--p-ref-gap-ext-penalty: INTEGER Range(1, None) Reference gap extend penalty. [default: 3]" min="1" name="prefgapextpenalty" optional="True" type="integer" value="3" />
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60 <param label="--p-no-exclude-seqs: Do not exclude sequences that align to reference. Set this option to False to exclude sequences that do not align to the reference database. [default: True]" name="pnoexcludeseqs" selected="False" type="boolean" />
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61 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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62
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63 </inputs>
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64
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65 <outputs>
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66 <data format="qza" label="${tool.name} on ${on_string}: filteredsequences.qza" name="ofilteredsequences" />
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67
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68 </outputs>
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69
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70 <help><![CDATA[
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71 Filter demultiplexed sequences by alignment to reference database.
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72 ###############################################################
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73
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74 Filter out (or keep) demultiplexed single- or paired-end sequences that
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75 align to a reference database, using bowtie2 and samtools. This method can
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76 be used to filter out human DNA sequences and other contaminants in any
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77 FASTQ sequence data (e.g., shotgun genome or amplicon sequence data), or
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78 alternatively (when exclude_seqs is False) to only keep sequences that do
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79 align to the reference.
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80
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81 Parameters
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82 ----------
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83 demultiplexed_sequences : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality²]
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84 The sequences to be trimmed.
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85 database : Bowtie2Index
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86 Bowtie2 indexed database.
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87 n_threads : Int % Range(1, None), optional
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88 Number of alignment threads to launch.
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89 mode : Str % Choices('local', 'global'), optional
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90 Bowtie2 alignment settings. See bowtie2 manual for more details.
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91 sensitivity : Str % Choices('very-fast', 'fast', 'sensitive', 'very-sensitive'), optional
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92 Bowtie2 alignment sensitivity. See bowtie2 manual for details.
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93 ref_gap_open_penalty : Int % Range(1, None), optional
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94 Reference gap open penalty.
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95 ref_gap_ext_penalty : Int % Range(1, None), optional
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96 Reference gap extend penalty.
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97 exclude_seqs : Bool, optional
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98 Exclude sequences that align to reference. Set this option to False to
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99 exclude sequences that do not align to the reference database.
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100
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101 Returns
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102 -------
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103 filtered_sequences : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality²]
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104 The resulting filtered sequences.
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105 ]]></help>
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106 <macros>
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107 <import>qiime_citation.xml</import>
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108 </macros>
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109 <expand macro="qiime_citation"/>
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110 </tool> |