|
14
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_quality-control_filter-reads" name="qiime quality-control filter-reads"
|
|
|
3 version="2020.8">
|
|
|
4 <description>Filter demultiplexed sequences by alignment to reference database.</description>
|
|
|
5 <requirements>
|
|
|
6 <requirement type="package" version="2020.8">qiime2</requirement>
|
|
|
7 </requirements>
|
|
|
8 <command><![CDATA[
|
|
|
9 qiime quality-control filter-reads
|
|
|
10
|
|
|
11 --i-demultiplexed-sequences=$idemultiplexedsequences
|
|
|
12
|
|
|
13 --i-database=$idatabase
|
|
|
14
|
|
|
15 --p-n-threads=$pnthreads
|
|
|
16
|
|
|
17 #if str($pmode) != 'None':
|
|
|
18 --p-mode=$pmode
|
|
|
19 #end if
|
|
|
20
|
|
|
21 #if str($psensitivity) != 'None':
|
|
|
22 --p-sensitivity=$psensitivity
|
|
|
23 #end if
|
|
|
24
|
|
|
25 --p-ref-gap-open-penalty=$prefgapopenpenalty
|
|
|
26
|
|
|
27 --p-ref-gap-ext-penalty=$prefgapextpenalty
|
|
|
28
|
|
|
29 #if $pnoexcludeseqs:
|
|
|
30 --p-no-exclude-seqs
|
|
|
31 #end if
|
|
|
32
|
|
|
33 --o-filtered-sequences=ofilteredsequences
|
|
|
34
|
|
|
35 #if str($examples) != 'None':
|
|
|
36 --examples=$examples
|
|
|
37 #end if
|
|
|
38
|
|
|
39 ;
|
|
|
40 cp ofilteredsequences.qza $ofilteredsequences
|
|
|
41
|
|
|
42 ]]></command>
|
|
|
43 <inputs>
|
|
|
44 <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality²] The sequences to be trimmed. [required]" name="idemultiplexedsequences" optional="False" type="data" />
|
|
|
45 <param format="qza,no_unzip.zip" label="--i-database: ARTIFACT Bowtie2 indexed database. Bowtie2Index [required]" name="idatabase" optional="False" type="data" />
|
|
|
46 <param label="--p-mode: " name="pmode" optional="True" type="select">
|
|
|
47 <option selected="True" value="None">Selection is Optional</option>
|
|
|
48 <option value="local">local</option>
|
|
|
49 <option value="global">global</option>
|
|
|
50 </param>
|
|
|
51 <param label="--p-sensitivity: " name="psensitivity" optional="True" type="select">
|
|
|
52 <option selected="True" value="None">Selection is Optional</option>
|
|
|
53 <option value="very-fast">very-fast</option>
|
|
|
54 <option value="fast">fast</option>
|
|
|
55 <option value="sensitive">sensitive</option>
|
|
|
56 <option value="very-sensitive">very-sensitive</option>
|
|
|
57 </param>
|
|
|
58 <param label="--p-ref-gap-open-penalty: INTEGER Range(1, None) Reference gap open penalty. [default: 5]" min="1" name="prefgapopenpenalty" optional="True" type="integer" value="5" />
|
|
|
59 <param label="--p-ref-gap-ext-penalty: INTEGER Range(1, None) Reference gap extend penalty. [default: 3]" min="1" name="prefgapextpenalty" optional="True" type="integer" value="3" />
|
|
|
60 <param label="--p-no-exclude-seqs: Do not exclude sequences that align to reference. Set this option to False to exclude sequences that do not align to the reference database. [default: True]" name="pnoexcludeseqs" selected="False" type="boolean" />
|
|
|
61 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
|
|
|
62
|
|
|
63 </inputs>
|
|
|
64
|
|
|
65 <outputs>
|
|
|
66 <data format="qza" label="${tool.name} on ${on_string}: filteredsequences.qza" name="ofilteredsequences" />
|
|
|
67
|
|
|
68 </outputs>
|
|
|
69
|
|
|
70 <help><![CDATA[
|
|
|
71 Filter demultiplexed sequences by alignment to reference database.
|
|
|
72 ###############################################################
|
|
|
73
|
|
|
74 Filter out (or keep) demultiplexed single- or paired-end sequences that
|
|
|
75 align to a reference database, using bowtie2 and samtools. This method can
|
|
|
76 be used to filter out human DNA sequences and other contaminants in any
|
|
|
77 FASTQ sequence data (e.g., shotgun genome or amplicon sequence data), or
|
|
|
78 alternatively (when exclude_seqs is False) to only keep sequences that do
|
|
|
79 align to the reference.
|
|
|
80
|
|
|
81 Parameters
|
|
|
82 ----------
|
|
|
83 demultiplexed_sequences : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality²]
|
|
|
84 The sequences to be trimmed.
|
|
|
85 database : Bowtie2Index
|
|
|
86 Bowtie2 indexed database.
|
|
|
87 n_threads : Int % Range(1, None), optional
|
|
|
88 Number of alignment threads to launch.
|
|
|
89 mode : Str % Choices('local', 'global'), optional
|
|
|
90 Bowtie2 alignment settings. See bowtie2 manual for more details.
|
|
|
91 sensitivity : Str % Choices('very-fast', 'fast', 'sensitive', 'very-sensitive'), optional
|
|
|
92 Bowtie2 alignment sensitivity. See bowtie2 manual for details.
|
|
|
93 ref_gap_open_penalty : Int % Range(1, None), optional
|
|
|
94 Reference gap open penalty.
|
|
|
95 ref_gap_ext_penalty : Int % Range(1, None), optional
|
|
|
96 Reference gap extend penalty.
|
|
|
97 exclude_seqs : Bool, optional
|
|
|
98 Exclude sequences that align to reference. Set this option to False to
|
|
|
99 exclude sequences that do not align to the reference database.
|
|
|
100
|
|
|
101 Returns
|
|
|
102 -------
|
|
|
103 filtered_sequences : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality²]
|
|
|
104 The resulting filtered sequences.
|
|
|
105 ]]></help>
|
|
|
106 <macros>
|
|
|
107 <import>qiime_citation.xml</import>
|
|
|
108 </macros>
|
|
|
109 <expand macro="qiime_citation"/>
|
|
|
110 </tool> |
