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comparison qiime2/qiime_gneiss_ilr-hierarchical.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_gneiss_ilr-hierarchical" name="qiime gneiss ilr-hierarchical" version="2019.7"> 2 <tool id="qiime_gneiss_ilr-hierarchical" name="qiime gneiss ilr-hierarchical"
3 <description> - Isometric Log-ratio Transform applied to a hierarchical clustering</description> 3 version="2020.8">
4 <requirements> 4 <description>Isometric Log-ratio Transform applied to a hierarchical clustering</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime gneiss ilr-hierarchical 9 qiime gneiss ilr-hierarchical
9 10
10 --i-table=$itable 11 --i-table=$itable
12
11 --i-tree=$itree 13 --i-tree=$itree
12 14
13 #if str($ppseudocount): 15 --p-pseudocount=$ppseudocount
14 --p-pseudocount=$ppseudocount 16
17 --o-balances=obalances
18
19 #if str($examples) != 'None':
20 --examples=$examples
15 #end if 21 #end if
16 22
17 --o-balances=obalances
18 ; 23 ;
19 cp obalances.qza $obalances 24 cp obalances.qza $obalances
20 ]]></command> 25
21 <inputs> 26 ]]></command>
22 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | Composition] The feature table containing the samples in which the ilr transform will be performed. [required]" name="itable" optional="False" type="data"/> 27 <inputs>
23 <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT A hierarchy of feature identifiers that defines the Hierarchy partitions of features. Each tip in the hierarchycorresponds to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. This assumes that all of the internal nodes in the tree have labels. [required]" name="itree" optional="False" type="data"/> 28 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | Composition] The feature table containing the samples in which the ilr transform will be performed. [required]" name="itable" optional="False" type="data" />
24 <param label="--p-pseudocount: NUMBER The value to add to zero counts in the feature table. [default: 0.5]" name="ppseudocount" optional="True" type="float" value="0.5"/> 29 <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT A hierarchy of feature identifiers that defines the Hierarchy partitions of features. Each tip in the hierarchycorresponds to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. This assumes that all of the internal nodes in the tree have labels. [required]" name="itree" optional="False" type="data" />
25 </inputs> 30 <param label="--p-pseudocount: NUMBER The value to add to zero counts in the feature table. [default: 0.5]" name="ppseudocount" optional="True" type="float" value="0.5" />
26 <outputs> 31 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
27 <data format="qza" label="${tool.name} on ${on_string}: balances.qza" name="obalances"/> 32
28 </outputs> 33 </inputs>
29 <help><![CDATA[ 34
35 <outputs>
36 <data format="qza" label="${tool.name} on ${on_string}: balances.qza" name="obalances" />
37
38 </outputs>
39
40 <help><![CDATA[
30 Isometric Log-ratio Transform applied to a hierarchical clustering 41 Isometric Log-ratio Transform applied to a hierarchical clustering
31 ################################################################## 42 ###############################################################
32 43
33 Calculate balances given a hierarchy. 44 Calculate balances given a hierarchy.
34 45
35 Parameters 46 Parameters
36 ---------- 47 ----------
49 60
50 Returns 61 Returns
51 ------- 62 -------
52 balances : FeatureTable[Balance] 63 balances : FeatureTable[Balance]
53 The resulting balances from the ilr transform. 64 The resulting balances from the ilr transform.
54 ]]></help> 65 ]]></help>
55 <macros> 66 <macros>
56 <import>qiime_citation.xml</import> 67 <import>qiime_citation.xml</import>
57 </macros> 68 </macros>
58 <expand macro="qiime_citation"/> 69 <expand macro="qiime_citation"/>
59 </tool> 70 </tool>