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1 <?xml version="1.0" ?>
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2 <tool id="qiime_quality-control_exclude-seqs" name="qiime quality-control exclude-seqs"
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3 version="2020.8">
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4 <description>Exclude sequences by alignment</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 exclude-seqs
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10
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11 --i-query-sequences=$iquerysequences
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12
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13 --i-reference-sequences=$ireferencesequences
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14
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15 #if str($pmethod) != 'None':
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16 --p-method=$pmethod
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17 #end if
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18
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19 --p-perc-identity=$ppercidentity
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20
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21 #if str($pevalue):
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22 --p-evalue=$pevalue
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23 #end if
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24 --p-perc-query-aligned=$ppercqueryaligned
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25
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26 --p-threads=$pthreads
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27
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28 #if str($pleftjustify) != 'None':
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29 --p-left-justify=$pleftjustify
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30 #end if
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31
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32 --o-sequence-hits=osequencehits
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33
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34 --o-sequence-misses=osequencemisses
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35
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36 #if str($examples) != 'None':
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37 --examples=$examples
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38 #end if
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39
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40 ;
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41 cp osequencemisses.qza $osequencemisses
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42
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43 ]]></command>
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44 <inputs>
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45 <param format="qza,no_unzip.zip" label="--i-query-sequences: ARTIFACT FeatureData[Sequence] Sequences to test for exclusion [required]" name="iquerysequences" optional="False" type="data" />
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46 <param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] Reference sequences to align against feature sequences [required]" name="ireferencesequences" optional="False" type="data" />
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47 <param label="--p-method: " name="pmethod" optional="True" type="select">
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48 <option selected="True" value="None">Selection is Optional</option>
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49 <option value="blast">blast</option>
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50 <option value="blastn-short">blastn-short</option>
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51 </param>
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52 <param exclude_max="False" label="--p-perc-identity: PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if percent identity to reference is lower. Must be in range [0.0, 1.0] [default: 0.97]" max="1.0" min="0.0" name="ppercidentity" optional="True" type="float" value="0.97" />
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53 <param label="--p-evalue: NUMBER BLAST expectation (E) value threshold for saving hits. Reject if E value is higher than threshold. This threshold is disabled by default. [optional]" name="pevalue" optional="False" type="text" />
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54 <param label="--p-perc-query-aligned: NUMBER Percent of query sequence that must align to reference in order to be accepted as a hit. [default: 0.97]" name="ppercqueryaligned" optional="True" type="float" value="0.97" />
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55 <param label="--p-left-justify: " name="pleftjustify" optional="True" type="select">
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56 <option selected="True" value="None">Selection is Optional</option>
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57 <option value="False">False</option>
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58 </param>
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59 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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60
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61 </inputs>
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62
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63 <outputs>
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64 <data format="qza" label="${tool.name} on ${on_string}: sequencehits.qza" name="osequencehits" />
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65 <data format="qza" label="${tool.name} on ${on_string}: sequencemisses.qza" name="osequencemisses" />
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66
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67 </outputs>
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68
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69 <help><![CDATA[
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70 Exclude sequences by alignment
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71 ###############################################################
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72
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73 This method aligns feature sequences to a set of reference sequences to
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74 identify sequences that hit/miss the reference within a specified
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75 perc_identity, evalue, and perc_query_aligned. This method could be used to
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76 define a positive filter, e.g., extract only feature sequences that align
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77 to a certain clade of bacteria; or to define a negative filter, e.g.,
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78 identify sequences that align to contaminant or human DNA sequences that
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79 should be excluded from subsequent analyses. Note that filtering is
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80 performed based on the perc_identity, perc_query_aligned, and evalue
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81 thresholds (the latter only if method==BLAST and an evalue is set). Set
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82 perc_identity==0 and/or perc_query_aligned==0 to disable these filtering
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83 thresholds as necessary.
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84
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85 Parameters
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86 ----------
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87 query_sequences : FeatureData[Sequence]
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88 Sequences to test for exclusion
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89 reference_sequences : FeatureData[Sequence]
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90 Reference sequences to align against feature sequences
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91 method : Str % Choices('blast', 'blastn-short')¹ | Str % Choices('vsearch')², optional
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92 Alignment method to use for matching feature sequences against
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93 reference sequences
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94 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
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95 Reject match if percent identity to reference is lower. Must be in
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96 range [0.0, 1.0]
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97 evalue : Float, optional
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98 BLAST expectation (E) value threshold for saving hits. Reject if E
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99 value is higher than threshold. This threshold is disabled by default.
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100 perc_query_aligned : Float, optional
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101 Percent of query sequence that must align to reference in order to be
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102 accepted as a hit.
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103 threads : Int % Range(1, None), optional
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104 Number of jobs to execute. Only applies to vsearch method.
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105 left_justify : Bool % Choices(False)¹ | Bool², optional
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106 Reject match if the pairwise alignment begins with gaps
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107
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108 Returns
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109 -------
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110 sequence_hits : FeatureData[Sequence]
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111 Subset of feature sequences that align to reference sequences
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112 sequence_misses : FeatureData[Sequence]
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113 Subset of feature sequences that do not align to reference sequences
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114 ]]></help>
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115 <macros>
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116 <import>qiime_citation.xml</import>
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117 </macros>
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118 <expand macro="qiime_citation"/>
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119 </tool> |
