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1 <?xml version="1.0" ?>
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2 <tool id="qiime_gneiss_lme-regression" name="qiime gneiss lme-regression" version="2019.4">
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3 <description> - Simplicial Linear mixed effects regression</description>
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4 <requirements>
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5 <requirement type="package" version="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime gneiss lme-regression
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9
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10 --i-table=$itable
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11 --i-tree=$itree
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12 --p-formula="$pformula"
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13 --p-groups="$pgroups"
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14
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15
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16 #if $input_files_mmetadatafile:
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17 #def list_dict_to_string(list_dict):
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18 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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19 #for d in list_dict[1:]:
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20 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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21 #end for
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22 #return $file_list
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23 #end def
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24 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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25 #end if
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26
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27
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28 --o-visualization=ovisualization
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29 ;
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30 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
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31 && cp -r out/* '$ovisualization.files_path'
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32 && mv '$ovisualization.files_path/index.html' '$ovisualization';
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33 ]]></command>
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34 <inputs>
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35 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Balance] The feature table containing the samples in which simplicial regression with mixed effect will be performed. [required]" name="itable" optional="False" type="data"/>
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36 <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT A hierarchy of feature identifiers where each tip Hierarchy corresponds 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. [required]" name="itree" optional="False" type="data"/>
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37 <param label="--p-formula: TEXT Statistical formula specifying the statistical model. In other words, a list of the metadata categories that will be used in the linear mixed effect model, typically separated by '+'. For more information see https://patsy.readthedocs.io/en/latest/API-reference.ht ml [required]" name="pformula" optional="False" type="text"/>
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38 <param label="--p-groups: TEXT [required]" name="pgroups" optional="False" type="text"/>
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4
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39
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40 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]">
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41 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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42 </repeat>
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43
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44 </inputs>
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45 <outputs>
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46 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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47 </outputs>
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48 <help><![CDATA[
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49 Simplicial Linear mixed effects regression
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50 ##########################################
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51
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52 Build and run linear mixed effects model on balances. Use LME over OLS when
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53 you have repeated measurements such as (timeseries).
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54
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55 Parameters
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56 ----------
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57 table : FeatureTable[Balance]
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58 The feature table containing the samples in which simplicial regression
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59 with mixed effect will be performed.
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60 tree : Hierarchy
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61 A hierarchy of feature identifiers where each tip corresponds to the
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62 feature identifiers in the table. This tree can contain tip ids that
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63 are not present in the table, but all feature ids in the table must be
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64 present in this tree.
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65 metadata : Metadata
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66 Metadata information that contains the covariates of interest.
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67 formula : Str
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68 Statistical formula specifying the statistical model. In other words, a
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69 list of the metadata categories that will be used in the linear mixed
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70 effect model, typically separated by "+". For more information see
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71 https://patsy.readthedocs.io/en/latest/API-reference.html
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72 groups : Str
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73 \
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74
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75 Returns
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76 -------
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77 visualization : Visualization
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78 ]]></help>
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79 <macros>
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80 <import>qiime_citation.xml</import>
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81 </macros>
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82 <expand macro="qiime_citation"/>
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83 </tool>
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