Mercurial > repos > florianbegusch > qiime2_wrappers

comparison qiime2/qiime_taxa_collapse.xml @ 0:51b9b6b57732 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:51b9b6b57732
1 <?xml version="1.0" ?>
2 <tool id="qiime_taxa_collapse" name="qiime taxa collapse" version="2018.4">
3 <description>- Collapse features by their taxonomy at the specified level</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime taxa collapse --p-level="$plevel"
10
11 #if str( $id_to_taxonomy_fp.selector ) == 'history'
12 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
13 --i-taxonomy '$tax'
14 #else:
15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
16 --i-taxonomy '$tax'
17 #end if
18
19 --i-table=$itable --o-collapsed-table=ocollapsedtable
20 #if str($cmdconfig) != 'None':
21 --cmd-config=$cmdconfig
22 #end if
23 ;
24 cp ocollapsedtable.qza $ocollapsedtable;
25 ]]>
26 </command>
27 <inputs>
28 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] Feature table to be collapsed. [required]" name="itable" optional="False" type="data"/>
29
30 <conditional name="id_to_taxonomy_fp" optional="True">
31 <param name="selector" type="select" label="Reference taxonomy to query">
32 <option value="cached">Public databases</option>
33 <option value="history">Databases from your history</option>
34 </param>
35 <when value="cached">
36 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
37 <options from_data_table="qiime_taxonomy" />
38 </param>
39 </when>
40 <when value="history">
41 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
42 </when>
43 </conditional>
44
45 <param label="--p-level: The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required]" name="plevel" optional="False" type="text"/>
46
47 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
48 </inputs>
49 <outputs>
50 <data format="qza" label="${tool.name} on ${on_string}: collapsed-table.qza" name="ocollapsedtable"/>
51 </outputs>
52 <help>
53 <![CDATA[
54 Collapse features by their taxonomy at the specified level
55 -----------------------------------------------------------
56
57 Collapse groups of features that have the same taxonomic assignment through
58 the specified level. The frequencies of all features will be summed when
59 they are collapsed.
60
61 Parameters
62 ----------
63 table : FeatureTable[Frequency]
64 Feature table to be collapsed.
65 taxonomy : FeatureData[Taxonomy]
66 Taxonomic annotations for features in the provided feature table. All
67 features in the feature table must have a corresponding taxonomic
68 annotation. Taxonomic annotations that are not present in the feature
69 table will be ignored.
70 level : Int
71 The taxonomic level at which the features should be collapsed. All
72 ouput features will have exactly this many levels of taxonomic
73 annotation.
74
75 Returns
76 -------
77 collapsed_table : FeatureTable[Frequency]
78 The resulting feature table, where all features are now taxonomic
79 annotations with the user-specified number of levels.
80 ]]>
81 </help>
82 <macros>
83 <import>qiime_citation.xml</import>
84 </macros>
85 <expand macro="qiime_citation" />
86 </tool>