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comparison qiime2-2020.8/qiime_gneiss_assign-ids.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_gneiss_assign-ids" name="qiime gneiss assign-ids"
3 version="2020.8">
4 <description>Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime gneiss assign-ids
10
11 --i-input-table=$iinputtable
12
13 --i-input-tree=$iinputtree
14
15 --o-output-table=ooutputtable
16
17 --o-output-tree=ooutputtree
18
19 #if str($examples) != 'None':
20 --examples=$examples
21 #end if
22
23 ;
24 cp ooutputtree.qza $ooutputtree
25
26 ]]></command>
27 <inputs>
28 <param format="qza,no_unzip.zip" label="--i-input-table: ARTIFACT FeatureTable[Frequency] The input table of counts. [required]" name="iinputtable" optional="False" type="data" />
29 <param format="qza,no_unzip.zip" label="--i-input-tree: ARTIFACT Phylogeny[Rooted] The input tree with potential missing ids. [required]" name="iinputtree" optional="False" type="data" />
30 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
31
32 </inputs>
33
34 <outputs>
35 <data format="qza" label="${tool.name} on ${on_string}: outputtable.qza" name="ooutputtable" />
36 <data format="qza" label="${tool.name} on ${on_string}: outputtree.qza" name="ooutputtree" />
37
38 </outputs>
39
40 <help><![CDATA[
41 Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.
42 ###############################################################
43
44
45 Assigns UUIDs to uniquely identify internal nodes in the tree. Also
46 corrects for polytomies to create strictly bifurcating trees and aligns the
47 table columns with the tree tip names
48
49 Parameters
50 ----------
51 input_table : FeatureTable[Frequency]
52 The input table of counts.
53 input_tree : Phylogeny[Rooted]
54 The input tree with potential missing ids.
55
56 Returns
57 -------
58 output_table : FeatureTable[Frequency]
59 A table with features matching the tree tips.
60 output_tree : Hierarchy
61 A tree with uniquely identifying ids.
62 ]]></help>
63 <macros>
64 <import>qiime_citation.xml</import>
65 </macros>
66 <expand macro="qiime_citation"/>
67 </tool>