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comparison qiime2-2020.8/qiime_quality-control_exclude-seqs.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_quality-control_exclude-seqs" name="qiime quality-control exclude-seqs"
3 version="2020.8">
4 <description>Exclude sequences by alignment</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime quality-control exclude-seqs
10
11 --i-query-sequences=$iquerysequences
12
13 --i-reference-sequences=$ireferencesequences
14
15 #if str($pmethod) != 'None':
16 --p-method=$pmethod
17 #end if
18
19 --p-perc-identity=$ppercidentity
20
21 #if str($pevalue):
22 --p-evalue=$pevalue
23 #end if
24 --p-perc-query-aligned=$ppercqueryaligned
25
26 --p-threads=$pthreads
27
28 #if str($pleftjustify) != 'None':
29 --p-left-justify=$pleftjustify
30 #end if
31
32 --o-sequence-hits=osequencehits
33
34 --o-sequence-misses=osequencemisses
35
36 #if str($examples) != 'None':
37 --examples=$examples
38 #end if
39
40 ;
41 cp osequencemisses.qza $osequencemisses
42
43 ]]></command>
44 <inputs>
45 <param format="qza,no_unzip.zip" label="--i-query-sequences: ARTIFACT FeatureData[Sequence] Sequences to test for exclusion [required]" name="iquerysequences" optional="False" type="data" />
46 <param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] Reference sequences to align against feature sequences [required]" name="ireferencesequences" optional="False" type="data" />
47 <param label="--p-method: " name="pmethod" optional="True" type="select">
48 <option selected="True" value="None">Selection is Optional</option>
49 <option value="blast">blast</option>
50 <option value="blastn-short">blastn-short</option>
51 </param>
52 <param exclude_max="False" label="--p-perc-identity: PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if percent identity to reference is lower. Must be in range [0.0, 1.0] [default: 0.97]" max="1.0" min="0.0" name="ppercidentity" optional="True" type="float" value="0.97" />
53 <param label="--p-evalue: NUMBER BLAST expectation (E) value threshold for saving hits. Reject if E value is higher than threshold. This threshold is disabled by default. [optional]" name="pevalue" optional="False" type="text" />
54 <param label="--p-perc-query-aligned: NUMBER Percent of query sequence that must align to reference in order to be accepted as a hit. [default: 0.97]" name="ppercqueryaligned" optional="True" type="float" value="0.97" />
55 <param label="--p-left-justify: " name="pleftjustify" optional="True" type="select">
56 <option selected="True" value="None">Selection is Optional</option>
57 <option value="False">False</option>
58 </param>
59 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
60
61 </inputs>
62
63 <outputs>
64 <data format="qza" label="${tool.name} on ${on_string}: sequencehits.qza" name="osequencehits" />
65 <data format="qza" label="${tool.name} on ${on_string}: sequencemisses.qza" name="osequencemisses" />
66
67 </outputs>
68
69 <help><![CDATA[
70 Exclude sequences by alignment
71 ###############################################################
72
73 This method aligns feature sequences to a set of reference sequences to
74 identify sequences that hit/miss the reference within a specified
75 perc_identity, evalue, and perc_query_aligned. This method could be used to
76 define a positive filter, e.g., extract only feature sequences that align
77 to a certain clade of bacteria; or to define a negative filter, e.g.,
78 identify sequences that align to contaminant or human DNA sequences that
79 should be excluded from subsequent analyses. Note that filtering is
80 performed based on the perc_identity, perc_query_aligned, and evalue
81 thresholds (the latter only if method==BLAST and an evalue is set). Set
82 perc_identity==0 and/or perc_query_aligned==0 to disable these filtering
83 thresholds as necessary.
84
85 Parameters
86 ----------
87 query_sequences : FeatureData[Sequence]
88 Sequences to test for exclusion
89 reference_sequences : FeatureData[Sequence]
90 Reference sequences to align against feature sequences
91 method : Str % Choices('blast', 'blastn-short')¹ | Str % Choices('vsearch')², optional
92 Alignment method to use for matching feature sequences against
93 reference sequences
94 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
95 Reject match if percent identity to reference is lower. Must be in
96 range [0.0, 1.0]
97 evalue : Float, optional
98 BLAST expectation (E) value threshold for saving hits. Reject if E
99 value is higher than threshold. This threshold is disabled by default.
100 perc_query_aligned : Float, optional
101 Percent of query sequence that must align to reference in order to be
102 accepted as a hit.
103 threads : Int % Range(1, None), optional
104 Number of jobs to execute. Only applies to vsearch method.
105 left_justify : Bool % Choices(False)¹ | Bool², optional
106 Reject match if the pairwise alignment begins with gaps
107
108 Returns
109 -------
110 sequence_hits : FeatureData[Sequence]
111 Subset of feature sequences that align to reference sequences
112 sequence_misses : FeatureData[Sequence]
113 Subset of feature sequences that do not align to reference sequences
114 ]]></help>
115 <macros>
116 <import>qiime_citation.xml</import>
117 </macros>
118 <expand macro="qiime_citation"/>
119 </tool>