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comparison qiime2/qiime_alignment_mask.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_alignment_mask" name="qiime alignment mask" version="2019.4">
3 <description> - Positional conservation and gap filtering.</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
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
22 cp omaskedalignment.qza $omaskedalignment
23 ]]></command>
24 <inputs>
25 <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] The alignment to be masked. [required]" name="ialignment" optional="False" type="data"/>
26 <param label="--p-max-gap-frequency: PROPORTION Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. [default: 1.0]" name="pmaxgapfrequency" optional="True" type="float" min="0" max="1" exclude_max="False" value="1.0"/>
27 <param label="--p-min-conservation: PROPORTION Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. [default: 0.4]" name="pminconservation" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.4"/>
28 </inputs>
29 <outputs>
30 <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment"/>
31 </outputs>
32 <help><![CDATA[
33 Positional conservation and gap filtering.
34 ##########################################
35
36 Mask (i.e., filter) unconserved and highly gapped columns from an
37 alignment. Default min_conservation was chosen to reproduce the mask
38 presented in Lane (1991).
39
40 Parameters
41 ----------
42 alignment : FeatureData[AlignedSequence]
43 The alignment to be masked.
44 max_gap_frequency : Float % Range(0, 1, inclusive_end=True), optional
45 The maximum relative frequency of gap characters in a column for the
46 column to be retained. This relative frequency must be a number between
47 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without
48 gap characters, and 1.0 retains all columns regardless of gap character
49 frequency.
50 min_conservation : Float % Range(0, 1, inclusive_end=True), optional
51 The minimum relative frequency of at least one non-gap character in a
52 column for that column to be retained. This relative frequency must be
53 a number between 0.0 and 1.0 (inclusive). For example, if a value of
54 0.4 is provided, a column will only be retained if it contains at least
55 one character that is present in at least 40% of the sequences.
56
57 Returns
58 -------
59 masked_alignment : FeatureData[AlignedSequence]
60 The masked alignment.
61 ]]></help>
62 <macros>
63 <import>qiime_citation.xml</import>
64 </macros>
65 <expand macro="qiime_citation"/>
66 </tool>