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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="2018.4">
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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="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 qiime quality-control exclude-seqs --i-reference-sequences=$ireferencesequences --i-query-sequences=$iquerysequences
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10 #if str($pevalue):
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11 --p-evalue="$pevalue"
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12 #end if
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13
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14 #if $ppercidentity:
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15 --p-perc-identity=$ppercidentity
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16 #end if
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17
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18 #if $ppercqueryaligned:
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19 --p-perc-query-aligned=$ppercqueryaligned
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20 #end if
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21
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22 #if str($cmdconfig) != 'None':
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23 --cmd-config=$cmdconfig
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24 #end if
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25 --o-sequence-hits=osequencehits --o-sequence-misses=osequencemisses
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26 #if str($pmethod) != 'None':
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27 --p-method=$pmethod
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28 #end if
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29
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30 #set $pthreads = '${GALAXY_SLOTS:-4}'
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31
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32 #if str($pthreads):
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33 --p-threads="$pthreads"
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34 #end if
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35 ;
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36 cp osequencehits.qza $osequencehits;
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37 cp osequencemisses.qza $osequencemisses;
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38 ]]>
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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: 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: FeatureData[Sequence] Reference sequences to align against feature sequences [required]" name="ireferencesequences" optional="False" type="data"/>
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43
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44 <param label="--p-method: Alignment method to use for matching feature
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45 sequences against reference sequences
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46 [default: blast]" name="pmethod" 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="vsearch">vsearch</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
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53 <param label="--p-perc-identity: 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"/>
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54 <param label="--p-evalue: 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="text"/>
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55 <param label="--p-perc-query-aligned: 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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56
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57 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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58 </inputs>
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59 <outputs>
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60 <data format="qza" label="${tool.name} on ${on_string}: sequence-hits.qza" name="osequencehits"/>
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61 <data format="qza" label="${tool.name} on ${on_string}: sequence-misses.qza" name="osequencemisses"/>
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62 </outputs>
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63 <help><![CDATA[
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64 Exclude sequences by alignment
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65 -------------------------------
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66
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67 This method aligns feature sequences to a set of reference sequences to
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68 identify sequences that hit/miss the reference within a specified
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69 perc_identity, evalue, and perc_query_aligned. This method could be used to
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70 define a positive filter, e.g., extract only feature sequences that align
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71 to a certain clade of bacteria; or to define a negative filter, e.g.,
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72 identify sequences that align to contaminant or human DNA sequences that
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73 should be excluded from subsequent analyses. Note that filtering is
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74 performed based on the perc_identity, perc_query_aligned, and evalue
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75 thresholds (the latter only if method==BLAST and an evalue is set). Set
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76 perc_identity==0 and/or perc_query_aligned==0 to disable these filtering
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77 thresholds as necessary.
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78
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79 Parameters
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80 ----------
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81 query_sequences : FeatureData[Sequence]
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82 Sequences to test for exclusion
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83 reference_sequences : FeatureData[Sequence]
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84 Reference sequences to align against feature sequences
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85 method : Str % Choices({'blast', 'blastn-short', 'vsearch'}), optional
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86 Alignment method to use for matching feature sequences against
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87 reference sequences
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88 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
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89 Reject match if percent identity to reference is lower. Must be in
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90 range [0.0, 1.0]
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91 evalue : Float, optional
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92 BLAST expectation (E) value threshold for saving hits. Reject if E
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93 value is higher than threshold. This threshold is disabled by default.
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94 perc_query_aligned : Float, optional
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95 Percent of query sequence that must align to reference in order to be
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96 accepted as a hit.
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97
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98 Returns
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99 -------
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100 sequence_hits : FeatureData[Sequence]
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101 Subset of feature sequences that align to reference sequences
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102 sequence_misses : FeatureData[Sequence]
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103 Subset of feature sequences that do not align to reference sequences
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104 ]]>
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105 </help>
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106 </tool>
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