Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_gneiss_correlation-clustering.xml @ 14:a0a8d77a991c draft
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author | florianbegusch |
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date | Thu, 03 Sep 2020 09:51:29 +0000 |
parents | f190567fe3f6 |
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13:887cd4ad8e16 | 14:a0a8d77a991c |
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1 <?xml version="1.0" ?> | 1 <?xml version="1.0" ?> |
2 <tool id="qiime_gneiss_correlation-clustering" name="qiime gneiss correlation-clustering" version="2019.7"> | 2 <tool id="qiime_gneiss_correlation-clustering" name="qiime gneiss correlation-clustering" |
3 <description> - Hierarchical clustering using feature correlation.</description> | 3 version="2020.8"> |
4 <requirements> | 4 <description>Hierarchical clustering using feature correlation.</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 correlation-clustering | 9 qiime gneiss correlation-clustering |
9 | 10 |
10 --i-table=$itable | 11 --i-table=$itable |
11 | 12 |
12 #if $ppseudocount: | 13 --p-pseudocount=$ppseudocount |
13 --p-pseudocount=$ppseudocount | 14 |
15 --o-clustering=oclustering | |
16 | |
17 #if str($examples) != 'None': | |
18 --examples=$examples | |
14 #end if | 19 #end if |
15 | 20 |
16 --o-clustering=oclustering | |
17 ; | 21 ; |
18 cp oclustering.qza $oclustering | 22 cp oclustering.qza $oclustering |
19 ]]></command> | 23 |
20 <inputs> | 24 ]]></command> |
21 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples in which the columns will be clustered. [required]" name="itable" optional="False" type="data"/> | 25 <inputs> |
22 <param label="--p-pseudocount: NUMBER The value to add to zero counts in the feature table. [default: 0.5]" name="ppseudocount" optional="True" type="float" value="0.5"/> | 26 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples in which the columns will be clustered. [required]" name="itable" optional="False" type="data" /> |
23 </inputs> | 27 <param label="--p-pseudocount: NUMBER The value to add to zero counts in the feature table. [default: 0.5]" name="ppseudocount" optional="True" type="float" value="0.5" /> |
24 <outputs> | 28 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> |
25 <data format="qza" label="${tool.name} on ${on_string}: clustering.qza" name="oclustering"/> | 29 |
26 </outputs> | 30 </inputs> |
27 <help><![CDATA[ | 31 |
32 <outputs> | |
33 <data format="qza" label="${tool.name} on ${on_string}: clustering.qza" name="oclustering" /> | |
34 | |
35 </outputs> | |
36 | |
37 <help><![CDATA[ | |
28 Hierarchical clustering using feature correlation. | 38 Hierarchical clustering using feature correlation. |
29 ################################################## | 39 ############################################################### |
30 | 40 |
31 Build a bifurcating tree that represents a hierarchical clustering of | 41 Build a bifurcating tree that represents a hierarchical clustering of |
32 features. The hiearchical clustering uses Ward hierarchical clustering | 42 features. The hiearchical clustering uses Ward hierarchical clustering |
33 based on the degree of proportionality between features. | 43 based on the degree of proportionality between features. |
34 | 44 |
45 clustering : Hierarchy | 55 clustering : Hierarchy |
46 A hierarchy of feature identifiers where each tip corresponds to the | 56 A hierarchy of feature identifiers where each tip corresponds to the |
47 feature identifiers in the table. This tree can contain tip ids that | 57 feature identifiers in the table. This tree can contain tip ids that |
48 are not present in the table, but all feature ids in the table must be | 58 are not present in the table, but all feature ids in the table must be |
49 present in this tree. | 59 present in this tree. |
50 ]]></help> | 60 ]]></help> |
51 <macros> | 61 <macros> |
52 <import>qiime_citation.xml</import> | 62 <import>qiime_citation.xml</import> |
53 </macros> | 63 </macros> |
54 <expand macro="qiime_citation"/> | 64 <expand macro="qiime_citation"/> |
55 </tool> | 65 </tool> |