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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" version="2019.7">
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3 <description> - ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier</description>
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4 <requirements>
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5 <requirement type="package" version="2019.7">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime feature-classifier classify-hybrid-vsearch-sklearn
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9
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10 --i-query=$iquery
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11 --i-reference-reads=$ireferencereads
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12 --i-reference-taxonomy=$ireferencetaxonomy
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13 --i-classifier=$iclassifier
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14
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15 #if str($pmaxaccepts) != 'None':
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16 --p-maxaccepts=$pmaxaccepts
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17 #end if
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18
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19 #if str($ppercidentity):
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20 --p-perc-identity=$ppercidentity
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21 #end if
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22
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23 #if str($pquerycov):
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24 --p-query-cov=$pquerycov
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25 #end if
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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 #if str($pminconsensus):
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32 --p-min-consensus=$pminconsensus
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33 #end if
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34
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35 #if str($pconfidence) != 'None':
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36 --p-confidence=$pconfidence
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37 #end if
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38
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39 #if str($preadorientation) != 'None':
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40 --p-read-orientation=$preadorientation
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41 #end if
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42
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43 #set $pthreads = '${GALAXY_SLOTS:-4}'
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44
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45 #if str($pthreads):
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46
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47 #if str($pthreads):
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48 --p-threads="$pthreads"
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49 #end if
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50
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51 #end if
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52
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53
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54 #if $pprefilter:
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55 --p-prefilter
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56 #end if
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57
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58 #if str($psamplesize):
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59 --p-sample-size=$psamplesize
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60 #end if
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61
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62 #if str($prandseed):
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63 --p-randseed=$prandseed
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64 #end if
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65
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66
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67 --o-classification=oclassification
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68
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69 ;
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70 cp oclassification.qza $oclassification
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71 ]]></command>
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72 <inputs>
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73 <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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74 <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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75 <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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76 <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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77 <param label="--p-maxaccepts: " name="pmaxaccepts" optional="True" type="select">
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78 <option selected="True" value="None">Selection is Optional</option>
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79 <option value="Int % Range(1">Int % Range(1</option>
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80 <option value="None">None</option>
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81 </param>
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82 <param 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]" name="ppercidentity" optional="True" type="float" value="0.5"/>
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83 <param 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]" name="pquerycov" optional="True" type="float" value="0.8"/>
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84 <param label="--p-strand: " name="pstrand" optional="True" type="select">
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85 <option selected="True" value="None">Selection is Optional</option>
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86 <option value="both">both</option>
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87 <option value="plus">plus</option>
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88 </param>
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89 <param 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]" name="pminconsensus" optional="True" type="float" value="0.51"/>
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90 <param label="--p-confidence: " name="pconfidence" optional="True" type="select">
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91 <option selected="True" value="None">Selection is Optional</option>
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92 <option value="Float % Range(0">Float % Range(0</option>
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93 <option value="1">1</option>
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94 <option value="inclusive_end=True">inclusive_end=True</option>
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95 </param>
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96 <param label="--p-read-orientation: " name="preadorientation" optional="True" type="select">
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97 <option selected="True" value="None">Selection is Optional</option>
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98 <option value="same">same</option>
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99 <option value="reverse-complement">reverse-complement</option>
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100 <option value="auto">auto</option>
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101 </param>
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102 <param label="--p-prefilter: --p-no-prefilter Toggle positive filter of query sequences on or off. [default: True]" name="pprefilter" selected="False" type="boolean"/>
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103 <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]" name="psamplesize" optional="True" type="integer" value="1000"/>
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104 <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]" name="prandseed" optional="True" type="integer" value="0"/>
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105 </inputs>
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106 <outputs>
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107 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
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108 </outputs>
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109 <help><![CDATA[
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110
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111 ]]></help>
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112 <macros>
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113 <import>qiime_citation.xml</import>
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114 </macros>
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115 <expand macro="qiime_citation"/>
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116 </tool>
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