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comparison qiime2/qiime_alignment_mask.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_alignment_mask" name="qiime alignment mask" version="2019.7"> 2 <tool id="qiime_alignment_mask" name="qiime alignment mask"
3 <description> - Positional conservation and gap filtering.</description> 3 version="2020.8">
4 <requirements> 4 <description>Positional conservation and gap filtering.</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime alignment mask 9 qiime alignment mask
9 10
10 --i-alignment=$ialignment 11 --i-alignment=$ialignment
11 12
13 --p-max-gap-frequency=$pmaxgapfrequency
14
15 --p-min-conservation=$pminconservation
16
12 --o-masked-alignment=omaskedalignment 17 --o-masked-alignment=omaskedalignment
13 18
14 #if $pmaxgapfrequency: 19 #if str($examples) != 'None':
15 --p-max-gap-frequency=$pmaxgapfrequency 20 --examples=$examples
16 #end if
17
18 #if $pminconservation:
19 --p-min-conservation=$pminconservation
20 #end if 21 #end if
21 22
22 ; 23 ;
23 cp omaskedalignment.qza $omaskedalignment 24 cp omaskedalignment.qza $omaskedalignment
24 ]]></command> 25
25 <inputs> 26 ]]></command>
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 <inputs>
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 format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] The alignment to be masked. [required]" name="ialignment" optional="False" type="data" />
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 <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" />
29 </inputs> 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" />
30 <outputs> 31 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
31 <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment"/> 32
32 </outputs> 33 </inputs>
33 <help><![CDATA[ 34
35 <outputs>
36 <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment" />
37
38 </outputs>
39
40 <help><![CDATA[
34 Positional conservation and gap filtering. 41 Positional conservation and gap filtering.
35 ########################################## 42 ###############################################################
36 43
37 Mask (i.e., filter) unconserved and highly gapped columns from an 44 Mask (i.e., filter) unconserved and highly gapped columns from an
38 alignment. Default min_conservation was chosen to reproduce the mask 45 alignment. Default min_conservation was chosen to reproduce the mask
39 presented in Lane (1991). 46 presented in Lane (1991).
40 47
57 64
58 Returns 65 Returns
59 ------- 66 -------
60 masked_alignment : FeatureData[AlignedSequence] 67 masked_alignment : FeatureData[AlignedSequence]
61 The masked alignment. 68 The masked alignment.
62 ]]></help> 69 ]]></help>
63 <macros> 70 <macros>
64 <import>qiime_citation.xml</import> 71 <import>qiime_citation.xml</import>
65 </macros> 72 </macros>
66 <expand macro="qiime_citation"/> 73 <expand macro="qiime_citation"/>
67 </tool> 74 </tool>