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1 <?xml version="1.0" ?>
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2 <tool id="qiime_feature-classifier_classify-hybrid-vsearch-sklearn" name="qiime feature-classifier classify-hybrid-vsearch-sklearn"
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3 version="2020.8">
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4 <description> ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier</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 feature-classifier classify-hybrid-vsearch-sklearn
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10
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11 --i-query=$iquery
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12
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13 --i-reference-reads=$ireferencereads
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14
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15 --i-reference-taxonomy=$ireferencetaxonomy
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16
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17 --i-classifier=$iclassifier
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18
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19 #if str($pmaxaccepts) != 'None':
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20 --p-maxaccepts=$pmaxaccepts
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21 #end if
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22
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23 --p-perc-identity=$ppercidentity
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24
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25 --p-query-cov=$pquerycov
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26
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27 #if str($pstrand) != 'None':
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28 --p-strand=$pstrand
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29 #end if
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30
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31 --p-min-consensus=$pminconsensus
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32
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33 #if str($pmaxhits) != 'None':
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34 --p-maxhits=$pmaxhits
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35 #end if
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36
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37 #if str($pmaxrejects) != 'None':
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38 --p-maxrejects=$pmaxrejects
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39 #end if
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40
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41 #if str($pconfidence) != 'None':
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42 --p-confidence=$pconfidence
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43 #end if
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44
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45 #if str($preadorientation) != 'None':
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46 --p-read-orientation=$preadorientation
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47 #end if
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48
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49 --p-threads=$pthreads
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50
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51 #if $pnoprefilter:
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52 --p-no-prefilter
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53 #end if
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54
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55 --p-sample-size=$psamplesize
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56
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57 --p-randseed=$prandseed
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58
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59 --o-classification=oclassification
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60
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61 #if str($examples) != 'None':
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62 --examples=$examples
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63 #end if
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64
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65 ;
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66 cp oclassification.qza $oclassification
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67
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68 ]]></command>
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69 <inputs>
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70 <param format="qza,no_unzip.zip" label="--i-query: ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically. [required]" name="iquery" optional="False" type="data" />
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71 <param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] reference sequences. [required]" name="ireferencereads" optional="False" type="data" />
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72 <param format="qza,no_unzip.zip" label="--i-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] reference taxonomy labels. [required]" name="ireferencetaxonomy" optional="False" type="data" />
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73 <param format="qza,no_unzip.zip" label="--i-classifier: ARTIFACT TaxonomicClassifier Pre-trained sklearn taxonomic classifier for classifying the reads. [required]" name="iclassifier" optional="False" type="data" />
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74 <param label="--p-maxaccepts: " name="pmaxaccepts" optional="True" type="select">
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75 <option selected="True" value="None">Selection is Optional</option>
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76 <option value="Int % Range(1">Int % Range(1</option>
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77 <option value="None">None</option>
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78 </param>
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79 <param exclude_max="False" label="--p-perc-identity: PROPORTION Range(0.0, 1.0, inclusive_end=True) Percent sequence similarity to use for PREFILTER. Reject match if percent identity to query is lower. Set to a lower value to perform a rough pre-filter. This parameter is ignored if `prefilter` is disabled. [default: 0.5]" max="1.0" min="0.0" name="ppercidentity" optional="True" type="float" value="0.5" />
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80 <param exclude_max="False" label="--p-query-cov: PROPORTION Range(0.0, 1.0, inclusive_end=True) Query coverage threshold to use for PREFILTER. Reject match if query alignment coverage per high-scoring pair is lower. Set to a lower value to perform a rough pre-filter. This parameter is ignored if `prefilter` is disabled. [default: 0.8]" max="1.0" min="0.0" name="pquerycov" optional="True" type="float" value="0.8" />
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81 <param label="--p-strand: " name="pstrand" optional="True" type="select">
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82 <option selected="True" value="None">Selection is Optional</option>
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83 <option value="both">both</option>
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84 <option value="plus">plus</option>
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85 </param>
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86 <param exclude_max="False" exclude_min="True" label="--p-min-consensus: NUMBER Range(0.5, 1.0, inclusive_start=False, inclusive_end=True) Minimum fraction of assignments must match top hit to be accepted as consensus assignment. [default: 0.51]" max="1.0" min="0.5" name="pminconsensus" optional="True" type="float" value="0.51" />
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87 <param label="--p-maxhits: " name="pmaxhits" optional="True" type="select">
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88 <option selected="True" value="None">Selection is Optional</option>
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89 <option value="Int % Range(1">Int % Range(1</option>
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90 <option value="None">None</option>
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91 </param>
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92 <param label="--p-maxrejects: " name="pmaxrejects" optional="True" type="select">
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93 <option selected="True" value="None">Selection is Optional</option>
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94 <option value="Int % Range(1">Int % Range(1</option>
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95 <option value="None">None</option>
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96 </param>
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97 <param label="--p-confidence: " name="pconfidence" optional="True" type="select">
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98 <option selected="True" value="None">Selection is Optional</option>
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99 <option value="Float % Range(0">Float % Range(0</option>
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100 <option value="1">1</option>
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101 <option value="inclusive_end=True">inclusive_end=True</option>
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102 </param>
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103 <param label="--p-read-orientation: " name="preadorientation" optional="True" type="select">
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104 <option selected="True" value="None">Selection is Optional</option>
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105 <option value="same">same</option>
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106 <option value="reverse-complement">reverse-complement</option>
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107 <option value="auto">auto</option>
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108 </param>
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109 <param label="--p-no-prefilter: Do not toggle positive filter of query sequences on or off. [default: True]" name="pnoprefilter" selected="False" type="boolean" />
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110 <param label="--p-sample-size: INTEGER Range(1, None) Randomly extract the given number of sequences from the reference database to use for prefiltering. This parameter is ignored if `prefilter` is disabled. [default: 1000]" min="1" name="psamplesize" optional="True" type="integer" value="1000" />
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111 <param label="--p-randseed: INTEGER Use integer as a seed for the pseudo-random generator Range(0, None) used during prefiltering. A given seed always produces the same output, which is useful for replicability. Set to 0 to use a pseudo-random seed. This parameter is ignored if `prefilter` is disabled. [default: 0]" min="0" name="prandseed" optional="True" type="integer" value="0" />
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112 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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113
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114 </inputs>
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115
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116 <outputs>
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117 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification" />
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118
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119 </outputs>
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120
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121 <help><![CDATA[
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122 ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier
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123 ###############################################################
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124
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125 NOTE: THIS PIPELINE IS AN ALPHA RELEASE. Please report bugs to
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126 https://forum.qiime2.org! Assign taxonomy to query sequences using hybrid
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127 classifier. First performs rough positive filter to remove artifact and
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128 low-coverage sequences (use "prefilter" parameter to toggle this step on or
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129 off). Second, performs VSEARCH exact match between query and
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130 reference_reads to find exact matches, followed by least common ancestor
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131 consensus taxonomy assignment from among maxaccepts top hits, min_consensus
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132 of which share that taxonomic assignment. Query sequences without an exact
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133 match are then classified with a pre-trained sklearn taxonomy classifier to
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134 predict the most likely taxonomic lineage.
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135
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136 Parameters
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137 ----------
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138 query : FeatureData[Sequence]
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139 Sequences to classify taxonomically.
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140 reference_reads : FeatureData[Sequence]
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141 reference sequences.
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142 reference_taxonomy : FeatureData[Taxonomy]
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143 reference taxonomy labels.
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144 classifier : TaxonomicClassifier
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145 Pre-trained sklearn taxonomic classifier for classifying the reads.
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146 maxaccepts : Int % Range(1, None) | Str % Choices('all'), optional
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147 Maximum number of hits to keep for each query. Set to "all" to keep all
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148 hits > perc_identity similarity. Note that if strand=both, maxaccepts
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149 will keep N hits for each direction (if searches in the opposite
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150 direction yield results that exceed the minimum perc_identity). In
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151 those cases use maxhits to control the total number of hits returned.
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152 This option works in pair with maxrejects. The search process sorts
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153 target sequences by decreasing number of k-mers they have in common
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154 with the query sequence, using that information as a proxy for sequence
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155 similarity. After pairwise alignments, if the first target sequence
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156 passes the acceptation criteria, it is accepted as best hit and the
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157 search process stops for that query. If maxaccepts is set to a higher
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158 value, more hits are accepted. If maxaccepts and maxrejects are both
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159 set to "all", the complete database is searched.
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160 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
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161 Percent sequence similarity to use for PREFILTER. Reject match if
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162 percent identity to query is lower. Set to a lower value to perform a
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163 rough pre-filter. This parameter is ignored if `prefilter` is disabled.
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164 query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional
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165 Query coverage threshold to use for PREFILTER. Reject match if query
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166 alignment coverage per high-scoring pair is lower. Set to a lower value
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167 to perform a rough pre-filter. This parameter is ignored if `prefilter`
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168 is disabled.
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169 strand : Str % Choices('both', 'plus'), optional
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170 Align against reference sequences in forward ("plus") or both
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171 directions ("both").
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172 min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional
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173 Minimum fraction of assignments must match top hit to be accepted as
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174 consensus assignment.
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175 maxhits : Int % Range(1, None) | Str % Choices('all'), optional
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176 maxrejects : Int % Range(1, None) | Str % Choices('all'), optional
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177 reads_per_batch : Int % Range(0, None), optional
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178 Number of reads to process in each batch for sklearn classification. If
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179 "auto", this parameter is autoscaled to min(number of query sequences /
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180 threads, 20000).
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181 confidence : Float % Range(0, 1, inclusive_end=True) | Str % Choices('disable'), optional
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182 Confidence threshold for limiting taxonomic depth. Set to "disable" to
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183 disable confidence calculation, or 0 to calculate confidence but not
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184 apply it to limit the taxonomic depth of the assignments.
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185 read_orientation : Str % Choices('same', 'reverse-complement', 'auto'), optional
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186 Direction of reads with respect to reference sequences in pre-trained
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187 sklearn classifier. same will cause reads to be classified unchanged;
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188 reverse-complement will cause reads to be reversed and complemented
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189 prior to classification. "auto" will autodetect orientation based on
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190 the confidence estimates for the first 100 reads.
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191 threads : Int % Range(1, None), optional
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192 Number of threads to use for job parallelization.
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193 prefilter : Bool, optional
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194 Toggle positive filter of query sequences on or off.
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195 sample_size : Int % Range(1, None), optional
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196 Randomly extract the given number of sequences from the reference
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197 database to use for prefiltering. This parameter is ignored if
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198 `prefilter` is disabled.
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199 randseed : Int % Range(0, None), optional
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200 Use integer as a seed for the pseudo-random generator used during
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201 prefiltering. A given seed always produces the same output, which is
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202 useful for replicability. Set to 0 to use a pseudo-random seed. This
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203 parameter is ignored if `prefilter` is disabled.
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204
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205 Returns
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206 -------
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207 classification : FeatureData[Taxonomy]
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208 The resulting taxonomy classifications.
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209 ]]></help>
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210 <macros>
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211 <import>qiime_citation.xml</import>
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212 </macros>
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213 <expand macro="qiime_citation"/>
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214 </tool> |
