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1 <?xml version="1.0" ?>
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2 <tool id="qiime_composition_ancom" name="qiime composition ancom" version="2019.4">
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3 <description> - Apply ANCOM to identify features that differ in abundance.</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 composition ancom
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9
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10 --i-table=$itable
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11
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12 #def list_dict_to_string(list_dict):
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13 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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14 #for d in list_dict[1:]:
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15 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
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16 #end for
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17 #return $file_list
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18 #end def
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19
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20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --m-metadata-column="$mmetadatacolumn"
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21
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22 #if str($pdifferencefunction) != 'None':
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23 --p-difference-function=$pdifferencefunction
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24 #end if
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25
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26 #if str($ptransformfunction) != 'None':
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27 --p-transform-function=$ptransformfunction
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28 #end if
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29
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30 --o-visualization=ovisualization;
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31
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32 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
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33 && cp -r out/* '$ovisualization.files_path'
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34 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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35 ]]></command>
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36 <inputs>
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37 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Composition] - The feature table to be used for ANCOM computation. [required]" name="itable" optional="False" type="data"/>
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38 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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39 <param format="tabular" label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data"/>
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40 </repeat>
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41 <param label="--m-metadata-column: MetadataColumn[Categorical] - Column from metadata file or artifact viewable as metadata. The categorical sample metadata column to test for differential abundance across. [required]" name="mmetadatacolumn" optional="False" type="text"/>
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42 <param label="--p-difference-function: " name="pdifferencefunction" optional="True" type="select">
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43 <option selected="True" value="None">Selection is Optional</option>
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44 <option value="mean_difference">mean_difference</option>
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45 <option value="f_statistic">f_statistic</option>
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46 </param>
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47 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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48 <param label="--p-transform-function: " name="ptransformfunction" optional="True" type="select">
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49 <option selected="True" value="None">Selection is Optional</option>
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50 <option value="log">log</option>
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51 <option value="clr">clr</option>
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52 <option value="sqrt">sqrt</option>
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53 </param>
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54 </inputs>
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55 <outputs>
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56 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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57 </outputs>
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58 <help><![CDATA[
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59 Apply ANCOM to identify features that differ in abundance.
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60 ##########################################################
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61
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62 Apply Analysis of Composition of Microbiomes (ANCOM) to identify features
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63 that are differentially abundant across groups.
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64
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65 Parameters
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66 ----------
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67 table : FeatureTable[Composition]
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68 The feature table to be used for ANCOM computation.
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69 metadata : MetadataColumn[Categorical]
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70 The categorical sample metadata column to test for differential
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71 abundance across.
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72 transform_function : Str % Choices('sqrt', 'log', 'clr'), optional
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73 The method applied to transform feature values before generating
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74 volcano plots.
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75 difference_function : Str % Choices('mean_difference', 'f_statistic'), optional
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76 The method applied to visualize fold difference in feature abundances
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77 across groups for volcano plots.
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78
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79 Returns
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80 -------
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81 visualization : Visualization
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82 ]]></help>
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83 <macros>
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84 <import>qiime_citation.xml</import>
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85 </macros>
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86 <expand macro="qiime_citation"/>
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87 </tool>
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