annotate qiime2/qiime_gneiss_assign-ids.xml @ 7:85b520815e85 draft

Uploaded
author florianbegusch
date Tue, 13 Aug 2019 07:53:59 -0400
parents 370e0b6e9826
children f190567fe3f6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
2 <tool id="qiime_gneiss_assign-ids" name="qiime gneiss assign-ids" version="2019.4">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.</description>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
4 <requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
5 <requirement type="package" version="2019.4">qiime2</requirement>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
6 </requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
7 <command><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
8 qiime gneiss assign-ids
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --i-input-table=$iinputtable
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11 --i-input-tree=$iinputtree
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
12
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13 --o-output-table=ooutputtable
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
14 --o-output-tree=ooutputtree
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
16 cp ooutputtable.qza $ooutputtable;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17 cp ooutputtree.qza $ooutputtree
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20 <param format="qza,no_unzip.zip" label="--i-input-table: ARTIFACT FeatureTable[Frequency] The input table of counts. [required]" name="iinputtable" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21 <param format="qza,no_unzip.zip" label="--i-input-tree: ARTIFACT Phylogeny[Rooted] The input tree with potential missing ids. [required]" name="iinputtree" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24 <data format="qza" label="${tool.name} on ${on_string}: outputtable.qza" name="ooutputtable"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25 <data format="qza" label="${tool.name} on ${on_string}: outputtree.qza" name="ooutputtree"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28 Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29 ##########################################################################################################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31 Assigns UUIDs to uniquely identify internal nodes in the tree. Also
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32 corrects for polytomies to create strictly bifurcating trees and aligns the
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33 table columns with the tree tip names
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37 input_table : FeatureTable[Frequency]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38 The input table of counts.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 input_tree : Phylogeny[Rooted]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 The input tree with potential missing ids.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
44 output_table : FeatureTable[Frequency]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
45 A table with features matching the tree tips.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
46 output_tree : Hierarchy
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
47 A tree with uniquely identifying ids.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
48 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
49 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
50 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
51 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
52 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
53 </tool>