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1 <?xml version="1.0" ?>
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2 <tool id="qiime_quality-filter_q-score-joined" name="qiime quality-filter q-score-joined" version="2019.4">
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3 <description> - Quality filter based on joined sequence quality scores.</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-filter q-score-joined
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9
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10 --i-demux=$idemux
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11
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12 #if $pminquality:
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13 --p-min-quality=$pminquality
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14 #end if
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15
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16 #if $pqualitywindow:
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17 --p-quality-window=$pqualitywindow
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18 #end if
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19
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20 #if $pminlengthfraction:
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21 --p-min-length-fraction=$pminlengthfraction
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22 #end if
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23
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24 #if $pmaxambiguous:
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25 --p-max-ambiguous=$pmaxambiguous
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26 #end if
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27
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28 --o-filtered-sequences=ofilteredsequences
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29 --o-filter-stats=ofilterstats
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30 ;
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31 cp ofilteredsequences.qza $ofilteredsequences;
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32 cp ofilterstats.qza $ofilterstats
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33 ]]></command>
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34 <inputs>
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35 <param format="qza,no_unzip.zip" label="--i-demux: ARTIFACT SampleData[JoinedSequencesWithQuality] The demultiplexed sequence data to be quality filtered. [required]" name="idemux" optional="False" type="data"/>
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36 <param label="--p-min-quality: INTEGER The minimum acceptable PHRED score. All PHRED scores less that this value are considered to be low PHRED scores. [default: 4]" name="pminquality" optional="True" type="integer" value="4"/>
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37 <param label="--p-quality-window: INTEGER The maximum number of low PHRED scores that can be observed in direct succession before truncating a sequence read. [default: 3]" name="pqualitywindow" optional="True" type="integer" value="3"/>
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38 <param label="--p-min-length-fraction: NUMBER The minimum length that a sequence read can be following truncation and still be retained. This length should be provided as a fraction of the input sequence length. [default: 0.75]" name="pminlengthfraction" optional="True" type="float" value="0.75"/>
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39 <param label="--p-max-ambiguous: INTEGER The maximum number of ambiguous (i.e., N) base calls. This is applied after trimming sequences based on `min-length-fraction`. [default: 0]" name="pmaxambiguous" optional="True" type="integer" value="0"/>
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40 </inputs>
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41 <outputs>
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42 <data format="qza" label="${tool.name} on ${on_string}: filteredsequences.qza" name="ofilteredsequences"/>
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43 <data format="qza" label="${tool.name} on ${on_string}: filterstats.qza" name="ofilterstats"/>
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44 </outputs>
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45 <help><![CDATA[
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46 Quality filter based on joined sequence quality scores.
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47 #######################################################
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48
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49 This method filters joined sequence based on quality scores and the
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50 presence of ambiguous base calls.
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51
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52 Parameters
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53 ----------
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54 demux : SampleData[JoinedSequencesWithQuality]
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55 The demultiplexed sequence data to be quality filtered.
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56 min_quality : Int, optional
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57 The minimum acceptable PHRED score. All PHRED scores less that this
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58 value are considered to be low PHRED scores.
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59 quality_window : Int, optional
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60 The maximum number of low PHRED scores that can be observed in direct
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61 succession before truncating a sequence read.
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62 min_length_fraction : Float, optional
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63 The minimum length that a sequence read can be following truncation and
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64 still be retained. This length should be provided as a fraction of the
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65 input sequence length.
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66 max_ambiguous : Int, optional
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67 The maximum number of ambiguous (i.e., N) base calls. This is applied
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68 after trimming sequences based on `min_length_fraction`.
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69
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70 Returns
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71 -------
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72 filtered_sequences : SampleData[JoinedSequencesWithQuality]
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73 The resulting quality-filtered sequences.
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74 filter_stats : QualityFilterStats
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75 Summary statistics of the filtering process.
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76 ]]></help>
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77 <macros>
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78 <import>qiime_citation.xml</import>
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79 </macros>
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80 <expand macro="qiime_citation"/>
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81 </tool>
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