Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2-2020.8/qiime_quality-filter_q-score.xml @ 20:d93d8888f0b0 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 12:44:24 +0000 |
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19:6c48f8d82424 | 20:d93d8888f0b0 |
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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> |