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comparison qiime2/qiime_taxa_filter-table.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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children 914fa4daf16a
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1 <?xml version="1.0" ?>
2 <tool id="qiime_taxa_filter-table" name="qiime taxa filter-table" version="2019.4">
3 <description> - Taxonomy-based feature table filter.</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime taxa filter-table
9
10 --i-table=$itable
11
12
13 #if str( $id_to_taxonomy_fp.selector ) == 'history'
14 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
15 --i-taxonomy '$tax'
16 #else:
17 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
18 --i-taxonomy '$tax'
19 #end if
20
21
22 #if str($pinclude):
23 --p-include="$pinclude"
24 #end if
25
26 #if str($pexclude):
27 --p-exclude="$pexclude"
28 #end if
29
30 #if str($pquerydelimiter):
31 --p-query-delimiter="$pquerydelimiter"
32 #end if
33
34 #if str($pmode) != 'None':
35 --p-mode=$pmode
36 #end if
37
38 --o-filtered-table=ofilteredtable
39 ;
40 cp ofilteredtable.qza $ofilteredtable
41 ]]></command>
42 <inputs>
43 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to be filtered. [required]" name="itable" optional="False" type="data"/>
44
45 <conditional name="id_to_taxonomy_fp" optional="True">
46 <param name="selector" type="select" label="Reference taxonomy to query">
47 <option value="cached">Public databases</option>
48 <option value="history">Databases from your history</option>
49 </param>
50 <when value="cached">
51 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
52 <options from_data_table="qiime_taxonomy" />
53 </param>
54 </when>
55 <when value="history">
56 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
57 </when>
58 </conditional>
59
60 <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="True" type="text"/>
61 <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="True" type="text"/>
62 <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="True" type="text" value="','"/>
63 <param label="--p-mode: " name="pmode" optional="True" type="select">
64 <option selected="True" value="None">Selection is Optional</option>
65 <option value="exact">exact</option>
66 <option value="contains">contains</option>
67 </param>
68 </inputs>
69 <outputs>
70 <data format="qza" label="${tool.name} on ${on_string}: filteredtable.qza" name="ofilteredtable"/>
71 </outputs>
72 <help><![CDATA[
73 Taxonomy-based feature table filter.
74 ####################################
75
76 This method filters features from a table based on their taxonomic
77 annotations. Features can be retained in the resulting table by specifying
78 one or more include search terms, and can be filtered out of the resulting
79 table by specifying one or more exclude search terms. If both include and
80 exclude are provided, the inclusion critera will be applied before the
81 exclusion critera. Either include or exclude terms (or both) must be
82 provided. Any samples that have a total frequency of zero after filtering
83 will be removed from the resulting table.
84
85 Parameters
86 ----------
87 table : FeatureTable[Frequency]
88 Feature table to be filtered.
89 taxonomy : FeatureData[Taxonomy]
90 Taxonomic annotations for features in the provided feature table. All
91 features in the feature table must have a corresponding taxonomic
92 annotation. Taxonomic annotations for features that are not present in
93 the feature table will be ignored.
94 include : Str, optional
95 One or more search terms that indicate which taxa should be included in
96 the resulting table. If providing more than one term, terms should be
97 delimited by the query-delimiter character. By default, all taxa will
98 be included.
99 exclude : Str, optional
100 One or more search terms that indicate which taxa should be excluded
101 from the resulting table. If providing more than one term, terms should
102 be delimited by the query-delimiter character. By default, no taxa will
103 be excluded.
104 query_delimiter : Str, optional
105 The string used to delimit multiple search terms provided to include or
106 exclude. This parameter should only need to be modified if the default
107 delimiter (a comma) is used in the provided taxonomic annotations.
108 mode : Str % Choices('exact', 'contains'), optional
109 Mode for determining if a search term matches a taxonomic annotation.
110 "contains" requires that the annotation has the term as a substring;
111 "exact" requires that the annotation is a perfect match to a search
112 term.
113
114 Returns
115 -------
116 filtered_table : FeatureTable[Frequency]
117 The taxonomy-filtered feature table.
118 ]]></help>
119 <macros>
120 <import>qiime_citation.xml</import>
121 </macros>
122 <expand macro="qiime_citation"/>
123 </tool>