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comparison qiime2-2020.8/qiime_taxa_collapse.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_collapse" name="qiime taxa collapse"
3 version="2020.8">
4 <description>Collapse features by their taxonomy at the specified level</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime taxa collapse
10
11 --i-table=$itable
12
13 --i-taxonomy=$itaxonomy
14
15 --p-level=$plevel
16
17 --o-collapsed-table=ocollapsedtable
18
19 #if str($examples) != 'None':
20 --examples=$examples
21 #end if
22
23 ;
24 cp ocollapsedtable.qza $ocollapsedtable
25
26 ]]></command>
27 <inputs>
28 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required]" name="itable" optional="False" type="data" />
29 <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required]" name="itaxonomy" optional="False" type="data" />
30 <param label="--p-level: INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required]" name="plevel" optional="False" type="text" />
31 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
32
33 </inputs>
34
35 <outputs>
36 <data format="qza" label="${tool.name} on ${on_string}: collapsedtable.qza" name="ocollapsedtable" />
37
38 </outputs>
39
40 <help><![CDATA[
41 Collapse features by their taxonomy at the specified level
42 ###############################################################
43
44 Collapse groups of features that have the same taxonomic assignment through
45 the specified level. The frequencies of all features will be summed when
46 they are collapsed.
47
48 Parameters
49 ----------
50 table : FeatureTable[Frequency]
51 Feature table to be collapsed.
52 taxonomy : FeatureData[Taxonomy]
53 Taxonomic annotations for features in the provided feature table. All
54 features in the feature table must have a corresponding taxonomic
55 annotation. Taxonomic annotations that are not present in the feature
56 table will be ignored.
57 level : Int
58 The taxonomic level at which the features should be collapsed. All
59 ouput features will have exactly this many levels of taxonomic
60 annotation.
61
62 Returns
63 -------
64 collapsed_table : FeatureTable[Frequency]
65 The resulting feature table, where all features are now taxonomic
66 annotations with the user-specified number of levels.
67 ]]></help>
68 <macros>
69 <import>qiime_citation.xml</import>
70 </macros>
71 <expand macro="qiime_citation"/>
72 </tool>