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comparison qiime2-2020.8/qiime_taxa_filter-table.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-table" name="qiime taxa filter-table"
3 version="2020.8">
4 <description>Taxonomy-based feature table filter.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime taxa filter-table
10
11 --i-table=$itable
12
13 --i-taxonomy=$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-table=ofilteredtable
29
30 #if str($examples) != 'None':
31 --examples=$examples
32 #end if
33
34 ;
35 cp ofilteredtable.qza $ofilteredtable
36
37 ]]></command>
38 <inputs>
39 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to be filtered. [required]" name="itable" 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 table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations for features that are not present in the feature table 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 table. 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 table. 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}: filteredtable.qza" name="ofilteredtable" />
55
56 </outputs>
57
58 <help><![CDATA[
59 Taxonomy-based feature table filter.
60 ###############################################################
61
62 This method filters features from a table based on their taxonomic
63 annotations. Features can be retained in the resulting table by specifying
64 one or more include search terms, and can be filtered out of the resulting
65 table by specifying one or more exclude search terms. If both include and
66 exclude are provided, the inclusion critera will be applied before the
67 exclusion critera. Either include or exclude terms (or both) must be
68 provided. Any samples that have a total frequency of zero after filtering
69 will be removed from the resulting table.
70
71 Parameters
72 ----------
73 table : FeatureTable[Frequency]
74 Feature table to be filtered.
75 taxonomy : FeatureData[Taxonomy]
76 Taxonomic annotations for features in the provided feature table. All
77 features in the feature table must have a corresponding taxonomic
78 annotation. Taxonomic annotations for features that are not present in
79 the feature table will be ignored.
80 include : Str, optional
81 One or more search terms that indicate which taxa should be included in
82 the resulting table. If providing more than one term, terms should be
83 delimited by the query-delimiter character. By default, all taxa will
84 be included.
85 exclude : Str, optional
86 One or more search terms that indicate which taxa should be excluded
87 from the resulting table. If providing more than one term, terms should
88 be delimited by the query-delimiter character. By default, no taxa will
89 be excluded.
90 query_delimiter : Str, optional
91 The string used to delimit multiple search terms provided to include or
92 exclude. This parameter should only need to be modified if the default
93 delimiter (a comma) is used in the provided taxonomic annotations.
94 mode : Str % Choices('exact', 'contains'), optional
95 Mode for determining if a search term matches a taxonomic annotation.
96 "contains" requires that the annotation has the term as a substring;
97 "exact" requires that the annotation is a perfect match to a search
98 term.
99
100 Returns
101 -------
102 filtered_table : FeatureTable[Frequency]
103 The taxonomy-filtered feature table.
104 ]]></help>
105 <macros>
106 <import>qiime_citation.xml</import>
107 </macros>
108 <expand macro="qiime_citation"/>
109 </tool>