|
0
|
1 <?xml version="1.0" ?>
|
|
9
|
2 <tool id="qiime_alignment_mask" name="qiime alignment mask" version="2019.7">
|
|
0
|
3 <description> - Positional conservation and gap filtering.</description>
|
|
|
4 <requirements>
|
|
9
|
5 <requirement type="package" version="2019.7">qiime2</requirement>
|
|
0
|
6 </requirements>
|
|
|
7 <command><![CDATA[
|
|
|
8 qiime alignment mask
|
|
|
9
|
|
|
10 --i-alignment=$ialignment
|
|
|
11
|
|
|
12 --o-masked-alignment=omaskedalignment
|
|
|
13
|
|
|
14 #if $pmaxgapfrequency:
|
|
|
15 --p-max-gap-frequency=$pmaxgapfrequency
|
|
|
16 #end if
|
|
|
17
|
|
|
18 #if $pminconservation:
|
|
|
19 --p-min-conservation=$pminconservation
|
|
|
20 #end if
|
|
|
21
|
|
4
|
22 ;
|
|
0
|
23 cp omaskedalignment.qza $omaskedalignment
|
|
|
24 ]]></command>
|
|
|
25 <inputs>
|
|
|
26 <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] The alignment to be masked. [required]" name="ialignment" optional="False" type="data"/>
|
|
|
27 <param label="--p-max-gap-frequency: PROPORTION Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. [default: 1.0]" name="pmaxgapfrequency" optional="True" type="float" min="0" max="1" exclude_max="False" value="1.0"/>
|
|
|
28 <param label="--p-min-conservation: PROPORTION Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. [default: 0.4]" name="pminconservation" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.4"/>
|
|
|
29 </inputs>
|
|
|
30 <outputs>
|
|
|
31 <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment"/>
|
|
|
32 </outputs>
|
|
|
33 <help><![CDATA[
|
|
|
34 Positional conservation and gap filtering.
|
|
|
35 ##########################################
|
|
|
36
|
|
|
37 Mask (i.e., filter) unconserved and highly gapped columns from an
|
|
|
38 alignment. Default min_conservation was chosen to reproduce the mask
|
|
|
39 presented in Lane (1991).
|
|
|
40
|
|
|
41 Parameters
|
|
|
42 ----------
|
|
|
43 alignment : FeatureData[AlignedSequence]
|
|
|
44 The alignment to be masked.
|
|
|
45 max_gap_frequency : Float % Range(0, 1, inclusive_end=True), optional
|
|
|
46 The maximum relative frequency of gap characters in a column for the
|
|
|
47 column to be retained. This relative frequency must be a number between
|
|
|
48 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without
|
|
|
49 gap characters, and 1.0 retains all columns regardless of gap character
|
|
|
50 frequency.
|
|
|
51 min_conservation : Float % Range(0, 1, inclusive_end=True), optional
|
|
|
52 The minimum relative frequency of at least one non-gap character in a
|
|
|
53 column for that column to be retained. This relative frequency must be
|
|
|
54 a number between 0.0 and 1.0 (inclusive). For example, if a value of
|
|
|
55 0.4 is provided, a column will only be retained if it contains at least
|
|
|
56 one character that is present in at least 40% of the sequences.
|
|
|
57
|
|
|
58 Returns
|
|
|
59 -------
|
|
|
60 masked_alignment : FeatureData[AlignedSequence]
|
|
|
61 The masked alignment.
|
|
|
62 ]]></help>
|
|
|
63 <macros>
|
|
|
64 <import>qiime_citation.xml</import>
|
|
|
65 </macros>
|
|
|
66 <expand macro="qiime_citation"/>
|
|
|
67 </tool>
|
