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1 <?xml version="1.0" ?>
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2 <tool id="qiime_quality-filter_q-score" name="qiime quality-filter q-score"
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3 version="2020.8">
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4 <description>Quality filter based on sequence quality scores.</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-filter q-score
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10
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11 --i-demux=$idemux
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12
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13 --p-min-quality=$pminquality
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14
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15 --p-quality-window=$pqualitywindow
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16
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17 --p-min-length-fraction=$pminlengthfraction
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18
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19 --p-max-ambiguous=$pmaxambiguous
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20
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21 --o-filtered-sequences=ofilteredsequences
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22
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23 --o-filter-stats=ofilterstats
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24
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25 #if str($examples) != 'None':
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26 --examples=$examples
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27 #end if
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28
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29 ;
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30 cp ofilterstats.qza $ofilterstats
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31
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32 ]]></command>
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33 <inputs>
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34 <param format="qza,no_unzip.zip" label="--i-demux: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]¹ | SampleData[JoinedSequencesWithQuality]² The demultiplexed sequence data to be quality filtered. [required]" name="idemux" optional="False" type="data" />
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35 <param label="--p-min-quality: INTEGER The minimum acceptable PHRED score. All PHRED scores less that this value are considered to be low PHRED scores. [default: 4]" name="pminquality" optional="True" type="integer" value="4" />
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36 <param label="--p-quality-window: INTEGER The maximum number of low PHRED scores that can be observed in direct succession before truncating a sequence read. [default: 3]" name="pqualitywindow" optional="True" type="integer" value="3" />
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37 <param label="--p-min-length-fraction: NUMBER The minimum length that a sequence read can be following truncation and still be retained. This length should be provided as a fraction of the input sequence length. [default: 0.75]" name="pminlengthfraction" optional="True" type="float" value="0.75" />
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38 <param label="--p-max-ambiguous: INTEGER The maximum number of ambiguous (i.e., N) base calls. This is applied after trimming sequences based on `min-length-fraction`. [default: 0]" name="pmaxambiguous" optional="True" type="integer" value="0" />
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39 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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40
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41 </inputs>
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42
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43 <outputs>
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44 <data format="qza" label="${tool.name} on ${on_string}: filteredsequences.qza" name="ofilteredsequences" />
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45 <data format="qza" label="${tool.name} on ${on_string}: filterstats.qza" name="ofilterstats" />
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46
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47 </outputs>
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48
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49 <help><![CDATA[
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50 Quality filter based on sequence quality scores.
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51 ###############################################################
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52
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53 This method filters sequence based on quality scores and the presence of
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54 ambiguous base calls.
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55
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56 Parameters
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57 ----------
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58 demux : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]¹ | SampleData[JoinedSequencesWithQuality]²
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59 The demultiplexed sequence data to be quality filtered.
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60 min_quality : Int, optional
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61 The minimum acceptable PHRED score. All PHRED scores less that this
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62 value are considered to be low PHRED scores.
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63 quality_window : Int, optional
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64 The maximum number of low PHRED scores that can be observed in direct
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65 succession before truncating a sequence read.
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66 min_length_fraction : Float, optional
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67 The minimum length that a sequence read can be following truncation and
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68 still be retained. This length should be provided as a fraction of the
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69 input sequence length.
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70 max_ambiguous : Int, optional
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71 The maximum number of ambiguous (i.e., N) base calls. This is applied
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72 after trimming sequences based on `min_length_fraction`.
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73
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74 Returns
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75 -------
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76 filtered_sequences : SampleData[SequencesWithQuality]¹ | SampleData[JoinedSequencesWithQuality]²
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77 The resulting quality-filtered sequences.
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78 filter_stats : QualityFilterStats
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79 Summary statistics of the filtering process.
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80 ]]></help>
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81 <macros>
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82 <import>qiime_citation.xml</import>
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83 </macros>
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84 <expand macro="qiime_citation"/>
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85 </tool> |
