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comparison qiime2/qiime_alignment_mask.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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28:c28331a63dfd 29:3ba9833030c1
1 <?xml version="1.0" ?>
2 <tool id="qiime_alignment_mask" name="qiime alignment mask"
3 version="2020.8">
4 <description>Positional conservation and gap filtering.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime alignment mask
10
11 --i-alignment=$ialignment
12
13 --p-max-gap-frequency=$pmaxgapfrequency
14
15 --p-min-conservation=$pminconservation
16
17 --o-masked-alignment=omaskedalignment
18
19 #if str($examples) != 'None':
20 --examples=$examples
21 #end if
22
23 ;
24 cp omaskedalignment.qza $omaskedalignment
25
26 ]]></command>
27 <inputs>
28 <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] The alignment to be masked. [required]" name="ialignment" optional="False" type="data" />
29 <param exclude_max="False" label="--p-max-gap-frequency: PROPORTION Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. [default: 1.0]" max="1" min="0" name="pmaxgapfrequency" optional="True" type="float" value="1.0" />
30 <param exclude_max="False" label="--p-min-conservation: PROPORTION Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. [default: 0.4]" max="1" min="0" name="pminconservation" optional="True" type="float" value="0.4" />
31 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
32
33 </inputs>
34
35 <outputs>
36 <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment" />
37
38 </outputs>
39
40 <help><![CDATA[
41 Positional conservation and gap filtering.
42 ###############################################################
43
44 Mask (i.e., filter) unconserved and highly gapped columns from an
45 alignment. Default min_conservation was chosen to reproduce the mask
46 presented in Lane (1991).
47
48 Parameters
49 ----------
50 alignment : FeatureData[AlignedSequence]
51 The alignment to be masked.
52 max_gap_frequency : Float % Range(0, 1, inclusive_end=True), optional
53 The maximum relative frequency of gap characters in a column for the
54 column to be retained. This relative frequency must be a number between
55 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without
56 gap characters, and 1.0 retains all columns regardless of gap character
57 frequency.
58 min_conservation : Float % Range(0, 1, inclusive_end=True), optional
59 The minimum relative frequency of at least one non-gap character in a
60 column for that column to be retained. This relative frequency must be
61 a number between 0.0 and 1.0 (inclusive). For example, if a value of
62 0.4 is provided, a column will only be retained if it contains at least
63 one character that is present in at least 40% of the sequences.
64
65 Returns
66 -------
67 masked_alignment : FeatureData[AlignedSequence]
68 The masked alignment.
69 ]]></help>
70 <macros>
71 <import>qiime_citation.xml</import>
72 </macros>
73 <expand macro="qiime_citation"/>
74 </tool>