annotate qiime2/qiime_quality-control_exclude-seqs.xml @ 14:a0a8d77a991c draft

Uploaded
author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
2 <tool id="qiime_quality-control_exclude-seqs" name="qiime quality-control exclude-seqs"
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
3 version="2020.8">
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
4 <description>Exclude sequences by alignment</description>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
5 <requirements>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
6 <requirement type="package" version="2020.8">qiime2</requirement>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
7 </requirements>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
8 <command><![CDATA[
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9 qiime quality-control exclude-seqs
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11 --i-query-sequences=$iquerysequences
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
12
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13 --i-reference-sequences=$ireferencesequences
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
14
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15 #if str($pmethod) != 'None':
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
16 --p-method=$pmethod
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
19 --p-perc-identity=$ppercidentity
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21 #if str($pevalue):
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
22 --p-evalue=$pevalue
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23 #end if
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
24 --p-perc-query-aligned=$ppercqueryaligned
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
26 --p-threads=$pthreads
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
28 #if str($pleftjustify) != 'None':
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
29 --p-left-justify=$pleftjustify
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32 --o-sequence-hits=osequencehits
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
33
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34 --o-sequence-misses=osequencemisses
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
35
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
36 #if str($examples) != 'None':
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
37 --examples=$examples
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
38 #end if
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
39
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41 cp osequencemisses.qza $osequencemisses
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
42
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
43 ]]></command>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
44 <inputs>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
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" />
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
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" />
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
47 <param label="--p-method: " name="pmethod" optional="True" type="select">
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
48 <option selected="True" value="None">Selection is Optional</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
49 <option value="blast">blast</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
50 <option value="blastn-short">blastn-short</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
51 </param>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
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" />
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
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" />
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
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" />
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
55 <param label="--p-left-justify: " name="pleftjustify" optional="True" type="select">
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
56 <option selected="True" value="None">Selection is Optional</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
57 <option value="False">False</option>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
58 </param>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
59 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
60
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
61 </inputs>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
62
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
63 <outputs>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
64 <data format="qza" label="${tool.name} on ${on_string}: sequencehits.qza" name="osequencehits" />
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
65 <data format="qza" label="${tool.name} on ${on_string}: sequencemisses.qza" name="osequencemisses" />
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
66
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
67 </outputs>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
68
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
69 <help><![CDATA[
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
70 Exclude sequences by alignment
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
71 ###############################################################
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
72
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
73 This method aligns feature sequences to a set of reference sequences to
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
74 identify sequences that hit/miss the reference within a specified
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
75 perc_identity, evalue, and perc_query_aligned. This method could be used to
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
76 define a positive filter, e.g., extract only feature sequences that align
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
77 to a certain clade of bacteria; or to define a negative filter, e.g.,
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
78 identify sequences that align to contaminant or human DNA sequences that
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
79 should be excluded from subsequent analyses. Note that filtering is
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
80 performed based on the perc_identity, perc_query_aligned, and evalue
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
81 thresholds (the latter only if method==BLAST and an evalue is set). Set
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
82 perc_identity==0 and/or perc_query_aligned==0 to disable these filtering
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
83 thresholds as necessary.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
84
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
85 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
86 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
87 query_sequences : FeatureData[Sequence]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
88 Sequences to test for exclusion
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
89 reference_sequences : FeatureData[Sequence]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
90 Reference sequences to align against feature sequences
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
91 method : Str % Choices('blast', 'blastn-short')¹ | Str % Choices('vsearch')², optional
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
92 Alignment method to use for matching feature sequences against
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
93 reference sequences
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
94 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
95 Reject match if percent identity to reference is lower. Must be in
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
96 range [0.0, 1.0]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
97 evalue : Float, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
98 BLAST expectation (E) value threshold for saving hits. Reject if E
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
99 value is higher than threshold. This threshold is disabled by default.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
100 perc_query_aligned : Float, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
101 Percent of query sequence that must align to reference in order to be
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
102 accepted as a hit.
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
103 threads : Int % Range(1, None), optional
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
104 Number of jobs to execute. Only applies to vsearch method.
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
105 left_justify : Bool % Choices(False)¹ | Bool², optional
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
106 Reject match if the pairwise alignment begins with gaps
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
107
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
108 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
109 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
110 sequence_hits : FeatureData[Sequence]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
111 Subset of feature sequences that align to reference sequences
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
112 sequence_misses : FeatureData[Sequence]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
113 Subset of feature sequences that do not align to reference sequences
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
114 ]]></help>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
115 <macros>
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
116 <import>qiime_citation.xml</import>
14
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
117 </macros>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
118 <expand macro="qiime_citation"/>
a0a8d77a991c Uploaded
florianbegusch
parents: 9
diff changeset
119 </tool>