Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_quality-control_filter-reads.xml @ 29:3ba9833030c1 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 13:12:49 +0000 |
parents | a0a8d77a991c |
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28:c28331a63dfd | 29:3ba9833030c1 |
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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> |