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1 <?xml version="1.0" ?>
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2 <tool id="qiime_composition_ancom" name="qiime composition ancom" version="2018.4">
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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="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8
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9 qiime composition ancom --i-table=$itable
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10
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11 #def list_dict_to_string(list_dict):
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12 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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13 #for d in list_dict[1:]:
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14 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
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15 #end for
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16 #return $file_list
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17 #end def
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18
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19 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --m-metadata-column="$mmetadatacolumn"
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20
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21 #if str($pdifferencefunction) != 'None':
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22 --p-difference-function=$pdifferencefunction
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23 #end if
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24
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25 #if str($cmdconfig) != 'None':
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26 --cmd-config=$cmdconfig
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27 #end if
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28
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29 #if str($ptransformfunction) != 'None':
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30 --p-transform-function=$ptransformfunction
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31 #end if
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32
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33 --o-visualization=ovisualization;
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34
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35 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
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36 && cp -r out/* '$ovisualization.files_path'
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37 && mv '$ovisualization.files_path/index.html' '$ovisualization';
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38
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39 ]]></command>
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40 <inputs>
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41 <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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42 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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43 <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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44 </repeat>
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45 <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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46 <param label="--p-difference-function: " name="pdifferencefunction" optional="True" type="select">
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47 <option selected="True" value="None">Selection is Optional</option>
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48 <option value="mean_difference">mean_difference</option>
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49 <option value="f_statistic">f_statistic</option>
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50 </param>
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51 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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52 <param label="--p-transform-function: " name="ptransformfunction" optional="True" type="select">
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53 <option selected="True" value="None">Selection is Optional</option>
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54 <option value="log">log</option>
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55 <option value="clr">clr</option>
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56 <option value="sqrt">sqrt</option>
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57 </param>
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58 </inputs>
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59 <outputs>
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60 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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61 </outputs>
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62 <help>
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63 <![CDATA[
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64 Apply ANCOM to identify features that differ in abundance.
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65 ----------------------------------------------------------
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66
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67 Apply Analysis of Composition of Microbiomes (ANCOM) to identify features
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68 that are differentially abundant across groups.
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69
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70 Parameters
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71 ----------
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72 table : FeatureTable[Composition]
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73 The feature table to be used for ANCOM computation.
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74 metadata : MetadataColumn[Categorical]
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75 The categorical sample metadata column to test for differential
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76 abundance across.
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77 transform_function : Str % Choices({'clr', 'log', 'sqrt'}), optional
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78 The method applied to transform feature values before generating
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79 volcano plots.
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80 difference_function : Str % Choices({'f_statistic', 'mean_difference'}), optional
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81 The method applied to visualize fold difference in feature abundances
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82 across groups for volcano plots.
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83
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84 Returns
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85 -------
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86 visualization : Visualization
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87
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88 ]]>
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89 </help>
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90 <macros>
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91 <import>qiime_citation.xml</import>
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92 </macros>
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93 <expand macro="qiime_citation" />
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94 </tool>
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