comparison qiime2-2020.8/qiime_taxa_filter-seqs.xml @ 20:d93d8888f0b0 draft

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author florianbegusch
date Fri, 04 Sep 2020 12:44:24 +0000
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19:6c48f8d82424 20:d93d8888f0b0
1 <?xml version="1.0" ?>
2 <tool id="qiime_taxa_filter-seqs" name="qiime taxa filter-seqs"
3 version="2020.8">
4 <description>Taxonomy-based feature sequence filter.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime taxa filter-seqs
10
11 --i-sequences=$isequences
12
13 --i-taxonomy=$itaxonomy
14
15 #if str($pinclude):
16 --p-include=$pinclude
17 #end if
18 #if str($pexclude):
19 --p-exclude=$pexclude
20 #end if
21 #if str($pquerydelimiter):
22 --p-query-delimiter=$pquerydelimiter
23 #end if
24 #if str($pmode) != 'None':
25 --p-mode=$pmode
26 #end if
27
28 --o-filtered-sequences=ofilteredsequences
29
30 #if str($examples) != 'None':
31 --examples=$examples
32 #end if
33
34 ;
35 cp ofilteredsequences.qza $ofilteredsequences
36
37 ]]></command>
38 <inputs>
39 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] Feature sequences to be filtered. [required]" name="isequences" optional="False" type="data" />
40 <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature sequences. All features in the feature sequences must have a corresponding taxonomic annotation. Taxonomic annotations for features that are not present in the feature sequences will be ignored. [required]" name="itaxonomy" optional="False" type="data" />
41 <param label="--p-include: TEXT One or more search terms that indicate which taxa should be included in the resulting sequences. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included. [optional]" name="pinclude" optional="False" type="text" />
42 <param label="--p-exclude: TEXT One or more search terms that indicate which taxa should be excluded from the resulting sequences. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded. [optional]" name="pexclude" optional="False" type="text" />
43 <param label="--p-query-delimiter: TEXT The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations. [default: \',\']" name="pquerydelimiter" optional="False" type="text" value="\',\'" />
44 <param label="--p-mode: " name="pmode" optional="True" type="select">
45 <option selected="True" value="None">Selection is Optional</option>
46 <option value="exact">exact</option>
47 <option value="contains">contains</option>
48 </param>
49 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
50
51 </inputs>
52
53 <outputs>
54 <data format="qza" label="${tool.name} on ${on_string}: filteredsequences.qza" name="ofilteredsequences" />
55
56 </outputs>
57
58 <help><![CDATA[
59 Taxonomy-based feature sequence filter.
60 ###############################################################
61
62 This method filters sequences based on their taxonomic annotations.
63 Features can be retained in the result by specifying one or more include
64 search terms, and can be filtered out of the result by specifying one or
65 more exclude search terms. If both include and exclude are provided, the
66 inclusion critera will be applied before the exclusion critera. Either
67 include or exclude terms (or both) must be provided.
68
69 Parameters
70 ----------
71 sequences : FeatureData[Sequence]
72 Feature sequences to be filtered.
73 taxonomy : FeatureData[Taxonomy]
74 Taxonomic annotations for features in the provided feature sequences.
75 All features in the feature sequences must have a corresponding
76 taxonomic annotation. Taxonomic annotations for features that are not
77 present in the feature sequences will be ignored.
78 include : Str, optional
79 One or more search terms that indicate which taxa should be included in
80 the resulting sequences. If providing more than one term, terms should
81 be delimited by the query-delimiter character. By default, all taxa
82 will be included.
83 exclude : Str, optional
84 One or more search terms that indicate which taxa should be excluded
85 from the resulting sequences. If providing more than one term, terms
86 should be delimited by the query-delimiter character. By default, no
87 taxa will be excluded.
88 query_delimiter : Str, optional
89 The string used to delimit multiple search terms provided to include or
90 exclude. This parameter should only need to be modified if the default
91 delimiter (a comma) is used in the provided taxonomic annotations.
92 mode : Str % Choices('exact', 'contains'), optional
93 Mode for determining if a search term matches a taxonomic annotation.
94 "contains" requires that the annotation has the term as a substring;
95 "exact" requires that the annotation is a perfect match to a search
96 term.
97
98 Returns
99 -------
100 filtered_sequences : FeatureData[Sequence]
101 The taxonomy-filtered feature sequences.
102 ]]></help>
103 <macros>
104 <import>qiime_citation.xml</import>
105 </macros>
106 <expand macro="qiime_citation"/>
107 </tool>