Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_quality-filter_q-score.xml @ 0:370e0b6e9826 draft
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author | florianbegusch |
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date | Wed, 17 Jul 2019 03:05:17 -0400 |
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children | de4c22a52df4 |
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1 <?xml version="1.0" ?> | |
2 <tool id="qiime_quality-filter_q-score" name="qiime quality-filter q-score" version="2019.4"> | |
3 <description> - Quality filter based on sequence quality scores.</description> | |
4 <requirements> | |
5 <requirement type="package" version="2019.4">qiime2</requirement> | |
6 </requirements> | |
7 <command><![CDATA[ | |
8 qiime quality-filter q-score | |
9 | |
10 --i-demux=$idemux | |
11 | |
12 #if $pminquality: | |
13 --p-min-quality=$pminquality | |
14 #end if | |
15 | |
16 #if $pqualitywindow: | |
17 --p-quality-window=$pqualitywindow | |
18 #end if | |
19 | |
20 #if $pminlengthfraction: | |
21 --p-min-length-fraction=$pminlengthfraction | |
22 #end if | |
23 | |
24 #if $pmaxambiguous: | |
25 --p-max-ambiguous=$pmaxambiguous | |
26 #end if | |
27 | |
28 --o-filtered-sequences=ofilteredsequences | |
29 --o-filter-stats=ofilterstats | |
30 ; | |
31 cp ofilteredsequences.qza $ofilteredsequences; | |
32 cp ofilterstats.qza $ofilterstats | |
33 ]]></command> | |
34 <inputs> | |
35 <param format="qza,no_unzip.zip" label="--i-demux: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality] The demultiplexed sequence data to be quality filtered. [required]" name="idemux" optional="False" type="data"/> | |
36 <param label="--p-min-quality: INTEGER The minimum acceptable PHRED score. All PHRED scores less that this value are considered to be low PHRED scores. [default: 4]" name="pminquality" optional="True" type="integer" value="4"/> | |
37 <param label="--p-quality-window: INTEGER The maximum number of low PHRED scores that can be observed in direct succession before truncating a sequence read. [default: 3]" name="pqualitywindow" optional="True" type="integer" value="3"/> | |
38 <param label="--p-min-length-fraction: NUMBER The minimum length that a sequence read can be following truncation and still be retained. This length should be provided as a fraction of the input sequence length. [default: 0.75]" name="pminlengthfraction" optional="True" type="float" value="0.75"/> | |
39 <param label="--p-max-ambiguous: INTEGER The maximum number of ambiguous (i.e., N) base calls. This is applied after trimming sequences based on `min-length-fraction`. [default: 0]" name="pmaxambiguous" optional="True" type="integer" value="0"/> | |
40 </inputs> | |
41 <outputs> | |
42 <data format="qza" label="${tool.name} on ${on_string}: filteredsequences.qza" name="ofilteredsequences"/> | |
43 <data format="qza" label="${tool.name} on ${on_string}: filterstats.qza" name="ofilterstats"/> | |
44 </outputs> | |
45 <help><![CDATA[ | |
46 Quality filter based on sequence quality scores. | |
47 ################################################ | |
48 | |
49 This method filters sequence based on quality scores and the presence of | |
50 ambiguous base calls. | |
51 | |
52 Parameters | |
53 ---------- | |
54 demux : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality] | |
55 The demultiplexed sequence data to be quality filtered. | |
56 min_quality : Int, optional | |
57 The minimum acceptable PHRED score. All PHRED scores less that this | |
58 value are considered to be low PHRED scores. | |
59 quality_window : Int, optional | |
60 The maximum number of low PHRED scores that can be observed in direct | |
61 succession before truncating a sequence read. | |
62 min_length_fraction : Float, optional | |
63 The minimum length that a sequence read can be following truncation and | |
64 still be retained. This length should be provided as a fraction of the | |
65 input sequence length. | |
66 max_ambiguous : Int, optional | |
67 The maximum number of ambiguous (i.e., N) base calls. This is applied | |
68 after trimming sequences based on `min_length_fraction`. | |
69 | |
70 Returns | |
71 ------- | |
72 filtered_sequences : SampleData[SequencesWithQuality] | |
73 The resulting quality-filtered sequences. | |
74 filter_stats : QualityFilterStats | |
75 Summary statistics of the filtering process. | |
76 ]]></help> | |
77 <macros> | |
78 <import>qiime_citation.xml</import> | |
79 </macros> | |
80 <expand macro="qiime_citation"/> | |
81 </tool> |