Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2-2020.8/qiime_gneiss_assign-ids.xml @ 20:d93d8888f0b0 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 12:44:24 +0000 |
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19:6c48f8d82424 | 20:d93d8888f0b0 |
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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> |