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comparison qiime2/qiime_gneiss_assign-ids.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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children f190567fe3f6
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-1:000000000000 0:370e0b6e9826
1 <?xml version="1.0" ?>
2 <tool id="qiime_gneiss_assign-ids" name="qiime gneiss assign-ids" version="2019.4">
3 <description> - Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime gneiss assign-ids
9
10 --i-input-table=$iinputtable
11 --i-input-tree=$iinputtree
12
13 --o-output-table=ooutputtable
14 --o-output-tree=ooutputtree
15 ;
16 cp ooutputtable.qza $ooutputtable;
17 cp ooutputtree.qza $ooutputtree
18 ]]></command>
19 <inputs>
20 <param format="qza,no_unzip.zip" label="--i-input-table: ARTIFACT FeatureTable[Frequency] The input table of counts. [required]" name="iinputtable" optional="False" type="data"/>
21 <param format="qza,no_unzip.zip" label="--i-input-tree: ARTIFACT Phylogeny[Rooted] The input tree with potential missing ids. [required]" name="iinputtree" optional="False" type="data"/>
22 </inputs>
23 <outputs>
24 <data format="qza" label="${tool.name} on ${on_string}: outputtable.qza" name="ooutputtable"/>
25 <data format="qza" label="${tool.name} on ${on_string}: outputtree.qza" name="ooutputtree"/>
26 </outputs>
27 <help><![CDATA[
28 Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.
29 ##########################################################################################################
30
31 Assigns UUIDs to uniquely identify internal nodes in the tree. Also
32 corrects for polytomies to create strictly bifurcating trees and aligns the
33 table columns with the tree tip names
34
35 Parameters
36 ----------
37 input_table : FeatureTable[Frequency]
38 The input table of counts.
39 input_tree : Phylogeny[Rooted]
40 The input tree with potential missing ids.
41
42 Returns
43 -------
44 output_table : FeatureTable[Frequency]
45 A table with features matching the tree tips.
46 output_tree : Hierarchy
47 A tree with uniquely identifying ids.
48 ]]></help>
49 <macros>
50 <import>qiime_citation.xml</import>
51 </macros>
52 <expand macro="qiime_citation"/>
53 </tool>