20
|
1 <?xml version="1.0" ?>
|
|
2 <tool id="qiime_quality-filter_q-score" name="qiime quality-filter q-score"
|
|
3 version="2020.8">
|
|
4 <description>Quality filter based on sequence quality scores.</description>
|
|
5 <requirements>
|
|
6 <requirement type="package" version="2020.8">qiime2</requirement>
|
|
7 </requirements>
|
|
8 <command><![CDATA[
|
|
9 qiime quality-filter q-score
|
|
10
|
|
11 --i-demux=$idemux
|
|
12
|
|
13 --p-min-quality=$pminquality
|
|
14
|
|
15 --p-quality-window=$pqualitywindow
|
|
16
|
|
17 --p-min-length-fraction=$pminlengthfraction
|
|
18
|
|
19 --p-max-ambiguous=$pmaxambiguous
|
|
20
|
|
21 --o-filtered-sequences=ofilteredsequences
|
|
22
|
|
23 --o-filter-stats=ofilterstats
|
|
24
|
|
25 #if str($examples) != 'None':
|
|
26 --examples=$examples
|
|
27 #end if
|
|
28
|
|
29 ;
|
|
30 cp ofilterstats.qza $ofilterstats
|
|
31
|
|
32 ]]></command>
|
|
33 <inputs>
|
|
34 <param format="qza,no_unzip.zip" label="--i-demux: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]¹ | SampleData[JoinedSequencesWithQuality]² The demultiplexed sequence data to be quality filtered. [required]" name="idemux" optional="False" type="data" />
|
|
35 <param label="--p-min-quality: INTEGER The minimum acceptable PHRED score. All PHRED scores less that this value are considered to be low PHRED scores. [default: 4]" name="pminquality" optional="True" type="integer" value="4" />
|
|
36 <param label="--p-quality-window: INTEGER The maximum number of low PHRED scores that can be observed in direct succession before truncating a sequence read. [default: 3]" name="pqualitywindow" optional="True" type="integer" value="3" />
|
|
37 <param label="--p-min-length-fraction: NUMBER The minimum length that a sequence read can be following truncation and still be retained. This length should be provided as a fraction of the input sequence length. [default: 0.75]" name="pminlengthfraction" optional="True" type="float" value="0.75" />
|
|
38 <param label="--p-max-ambiguous: INTEGER The maximum number of ambiguous (i.e., N) base calls. This is applied after trimming sequences based on `min-length-fraction`. [default: 0]" name="pmaxambiguous" optional="True" type="integer" value="0" />
|
|
39 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
|
|
40
|
|
41 </inputs>
|
|
42
|
|
43 <outputs>
|
|
44 <data format="qza" label="${tool.name} on ${on_string}: filteredsequences.qza" name="ofilteredsequences" />
|
|
45 <data format="qza" label="${tool.name} on ${on_string}: filterstats.qza" name="ofilterstats" />
|
|
46
|
|
47 </outputs>
|
|
48
|
|
49 <help><![CDATA[
|
|
50 Quality filter based on sequence quality scores.
|
|
51 ###############################################################
|
|
52
|
|
53 This method filters sequence based on quality scores and the presence of
|
|
54 ambiguous base calls.
|
|
55
|
|
56 Parameters
|
|
57 ----------
|
|
58 demux : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]¹ | SampleData[JoinedSequencesWithQuality]²
|
|
59 The demultiplexed sequence data to be quality filtered.
|
|
60 min_quality : Int, optional
|
|
61 The minimum acceptable PHRED score. All PHRED scores less that this
|
|
62 value are considered to be low PHRED scores.
|
|
63 quality_window : Int, optional
|
|
64 The maximum number of low PHRED scores that can be observed in direct
|
|
65 succession before truncating a sequence read.
|
|
66 min_length_fraction : Float, optional
|
|
67 The minimum length that a sequence read can be following truncation and
|
|
68 still be retained. This length should be provided as a fraction of the
|
|
69 input sequence length.
|
|
70 max_ambiguous : Int, optional
|
|
71 The maximum number of ambiguous (i.e., N) base calls. This is applied
|
|
72 after trimming sequences based on `min_length_fraction`.
|
|
73
|
|
74 Returns
|
|
75 -------
|
|
76 filtered_sequences : SampleData[SequencesWithQuality]¹ | SampleData[JoinedSequencesWithQuality]²
|
|
77 The resulting quality-filtered sequences.
|
|
78 filter_stats : QualityFilterStats
|
|
79 Summary statistics of the filtering process.
|
|
80 ]]></help>
|
|
81 <macros>
|
|
82 <import>qiime_citation.xml</import>
|
|
83 </macros>
|
|
84 <expand macro="qiime_citation"/>
|
|
85 </tool> |