Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_gneiss_assign-ids.xml @ 0:370e0b6e9826 draft
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author | florianbegusch |
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date | Wed, 17 Jul 2019 03:05:17 -0400 |
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children | f190567fe3f6 |
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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> |