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1 <?xml version="1.0" ?>
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2 <tool id="qiime_gneiss_gradient-clustering" name="qiime gneiss gradient-clustering"
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3 version="2020.8">
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4 <description>Hierarchical clustering using gradient information.</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime gneiss gradient-clustering
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10
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11 --i-table=$itable
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12
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13 #if str($mgradientfile) != 'None':
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14 --m-gradient-file=$mgradientfile
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15 #end if
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16
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17 #if '__ob__' in str($mgradientcolumn):
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18 #set $mgradientcolumn_temp = $mgradientcolumn.replace('__ob__', '[')
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19 #set $mgradientcolumn = $mgradientcolumn_temp
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20 #end if
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21 #if '__cb__' in str($mgradientcolumn):
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22 #set $mgradientcolumn_temp = $mgradientcolumn.replace('__cb__', ']')
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23 #set $mgradientcolumn = $mgradientcolumn_temp
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24 #end if
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25 #if 'X' in str($mgradientcolumn):
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26 #set $mgradientcolumn_temp = $mgradientcolumn.replace('X', '\\')
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27 #set $mgradientcolumn = $mgradientcolumn_temp
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28 #end if
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29 #if '__sq__' in str($mgradientcolumn):
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30 #set $mgradientcolumn_temp = $mgradientcolumn.replace('__sq__', "'")
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31 #set $mgradientcolumn = $mgradientcolumn_temp
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32 #end if
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33 #if '__db__' in str($mgradientcolumn):
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34 #set $mgradientcolumn_temp = $mgradientcolumn.replace('__db__', '"')
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35 #set $mgradientcolumn = $mgradientcolumn_temp
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36 #end if
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37
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38 --m-gradient-column=$mgradientcolumn
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39
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40
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41 #if $pignoremissingsamples:
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42 --p-ignore-missing-samples
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43 #end if
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44
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45 #if $pnoweighted:
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46 --p-no-weighted
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47 #end if
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48
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49 --o-clustering=oclustering
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50
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51 #if str($examples) != 'None':
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52 --examples=$examples
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53 #end if
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54
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55 ;
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56 cp oclustering.qza $oclustering
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57
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58 ]]></command>
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59 <inputs>
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60 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | Composition] The feature table containing the samples in which the columns will be clustered. [required]" name="itable" optional="False" type="data" />
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61 <param format="tabular,qza,no_unzip.zip" label="--m-gradient-file: METADATA" name="mgradientfile" optional="False" type="data" />
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62 <param label="--m-gradient-column: COLUMN MetadataColumn[Numeric] Contains gradient values to sort the features and samples. [required]" name="mgradientcolumn" optional="False" type="text" />
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63 <param label="--p-ignore-missing-samples: --p-ignore-missing-samples: / --p-no-ignore-missing-samples [default: False]" name="pignoremissingsamples" selected="False" type="boolean" />
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64 <param label="--p-no-weighted: Do not specifies if abundance or presence/absence information should be used to perform the clustering. [default: True]" name="pnoweighted" selected="False" type="boolean" />
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65 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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66
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67 </inputs>
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68
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69 <outputs>
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70 <data format="qza" label="${tool.name} on ${on_string}: clustering.qza" name="oclustering" />
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71
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72 </outputs>
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73
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74 <help><![CDATA[
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75 Hierarchical clustering using gradient information.
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76 ###############################################################
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77
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78 Build a bifurcating tree that represents a hierarchical clustering of
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79 features. The hiearchical clustering uses Ward hierarchical clustering
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80 based on the mean difference of gradients that each feature is observed in.
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81 This method is primarily used to sort the table to reveal the underlying
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82 block-like structures.
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83
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84 Parameters
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85 ----------
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86 table : FeatureTable[Frequency | RelativeFrequency | Composition]
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87 The feature table containing the samples in which the columns will be
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88 clustered.
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89 gradient : MetadataColumn[Numeric]
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90 Contains gradient values to sort the features and samples.
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91 ignore_missing_samples : Bool, optional
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92 weighted : Bool, optional
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93 Specifies if abundance or presence/absence information should be used
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94 to perform the clustering.
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95
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96 Returns
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97 -------
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98 clustering : Hierarchy
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99 A hierarchy of feature identifiers where each tip corresponds to the
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100 feature identifiers in the table. This tree can contain tip ids that
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101 are not present in the table, but all feature ids in the table must be
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102 present in this tree.
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103 ]]></help>
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104 <macros>
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105 <import>qiime_citation.xml</import>
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106 </macros>
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107 <expand macro="qiime_citation"/>
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108 </tool> |
