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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" version="2019.4">
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3 <description> - Exclude sequences by alignment</description>
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4 <requirements>
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5 <requirement type="package" version="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime quality-control exclude-seqs
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9
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10 --i-query-sequences=$iquerysequences
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11 --i-reference-sequences=$ireferencesequences
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12
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13 #if str($pmethod) != 'None':
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14 --p-method=$pmethod
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15 #end if
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16
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5
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17 #if str($ppercidentity):
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0
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18 --p-perc-identity=$ppercidentity
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19 #end if
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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
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5
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25 #if str($ppercqueryaligned):
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0
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26 --p-perc-query-aligned=$ppercqueryaligned
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27 #end if
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28
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29 #set $pthreads = '${GALAXY_SLOTS:-4}'
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30 #if str($pthreads):
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31 --p-threads="$pthreads"
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32 #end if
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33
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34 --o-sequence-hits=osequencehits
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35 --o-sequence-misses=osequencemisses
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36 ;
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37 cp osequencehits.qza $osequencehits;
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38 cp osequencemisses.qza $osequencemisses
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39 ]]></command>
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40 <inputs>
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41 <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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42 <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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43 <param label="--p-method: " name="pmethod" optional="True" type="select">
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44 <option selected="True" value="None">Selection is Optional</option>
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45 <option value="blast">blast</option>
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46 <option value="vsearch">vsearch</option>
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47 <option value="blastn-short">blastn-short</option>
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48 </param>
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49 <param 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]" name="ppercidentity" optional="True" type="float" value="0.97" min="0" max="1" exclusive_end="False"/>
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5
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50 <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="True" type="float"/>
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0
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51 <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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52 </inputs>
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53 <outputs>
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54 <data format="qza" label="${tool.name} on ${on_string}: sequencehits.qza" name="osequencehits"/>
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55 <data format="qza" label="${tool.name} on ${on_string}: sequencemisses.qza" name="osequencemisses"/>
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56 </outputs>
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57 <help><![CDATA[
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58 Exclude sequences by alignment
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59 ##############################
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60
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61 This method aligns feature sequences to a set of reference sequences to
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62 identify sequences that hit/miss the reference within a specified
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63 perc_identity, evalue, and perc_query_aligned. This method could be used to
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64 define a positive filter, e.g., extract only feature sequences that align
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65 to a certain clade of bacteria; or to define a negative filter, e.g.,
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66 identify sequences that align to contaminant or human DNA sequences that
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67 should be excluded from subsequent analyses. Note that filtering is
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68 performed based on the perc_identity, perc_query_aligned, and evalue
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69 thresholds (the latter only if method==BLAST and an evalue is set). Set
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70 perc_identity==0 and/or perc_query_aligned==0 to disable these filtering
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71 thresholds as necessary.
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72
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73 Parameters
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74 ----------
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75 query_sequences : FeatureData[Sequence]
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76 Sequences to test for exclusion
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77 reference_sequences : FeatureData[Sequence]
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78 Reference sequences to align against feature sequences
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79 method : Str % Choices('blast', 'vsearch', 'blastn-short'), optional
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80 Alignment method to use for matching feature sequences against
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81 reference sequences
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82 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
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83 Reject match if percent identity to reference is lower. Must be in
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84 range [0.0, 1.0]
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85 evalue : Float, optional
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86 BLAST expectation (E) value threshold for saving hits. Reject if E
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87 value is higher than threshold. This threshold is disabled by default.
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88 perc_query_aligned : Float, optional
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89 Percent of query sequence that must align to reference in order to be
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90 accepted as a hit.
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91
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92 Returns
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93 -------
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94 sequence_hits : FeatureData[Sequence]
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95 Subset of feature sequences that align to reference sequences
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96 sequence_misses : FeatureData[Sequence]
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97 Subset of feature sequences that do not align to reference sequences
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98 ]]></help>
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99 <macros>
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100 <import>qiime_citation.xml</import>
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101 </macros>
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102 <expand macro="qiime_citation"/>
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103 </tool>
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