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+ − 1 <?xml version="1.0" ?>
+ − 2 <tool id="qiime_composition_ancom" name="qiime composition ancom" version="2018.4">
+ − 3 <description> - Apply ANCOM to identify features that differ in abundance.</description>
+ − 4 <requirements>
+ − 5 <requirement type="package" version="2018.4">qiime2</requirement>
+ − 6 </requirements>
+ − 7 <command><![CDATA[
+ − 8
+ − 9 qiime composition ancom --i-table=$itable
+ − 10
+ − 11 #def list_dict_to_string(list_dict):
+ − 12 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
+ − 13 #for d in list_dict[1:]:
+ − 14 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
+ − 15 #end for
+ − 16 #return $file_list
+ − 17 #end def
+ − 18
+ − 19 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --m-metadata-column="$mmetadatacolumn"
+ − 20
+ − 21 #if str($pdifferencefunction) != 'None':
+ − 22 --p-difference-function=$pdifferencefunction
+ − 23 #end if
+ − 24
+ − 25 #if str($cmdconfig) != 'None':
+ − 26 --cmd-config=$cmdconfig
+ − 27 #end if
+ − 28
+ − 29 #if str($ptransformfunction) != 'None':
+ − 30 --p-transform-function=$ptransformfunction
+ − 31 #end if
+ − 32
+ − 33 --o-visualization=ovisualization;
+ − 34
+ − 35 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
+ − 36 && cp -r out/* '$ovisualization.files_path'
+ − 37 && mv '$ovisualization.files_path/index.html' '$ovisualization';
+ − 38
+ − 39 ]]></command>
+ − 40 <inputs>
+ − 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"/>
+ − 42 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
+ − 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"/>
+ − 44 </repeat>
+ − 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"/>
+ − 46 <param label="--p-difference-function: " name="pdifferencefunction" optional="True" type="select">
+ − 47 <option selected="True" value="None">Selection is Optional</option>
+ − 48 <option value="mean_difference">mean_difference</option>
+ − 49 <option value="f_statistic">f_statistic</option>
+ − 50 </param>
+ − 51 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
+ − 52 <param label="--p-transform-function: " name="ptransformfunction" optional="True" type="select">
+ − 53 <option selected="True" value="None">Selection is Optional</option>
+ − 54 <option value="log">log</option>
+ − 55 <option value="clr">clr</option>
+ − 56 <option value="sqrt">sqrt</option>
+ − 57 </param>
+ − 58 </inputs>
+ − 59 <outputs>
+ − 60 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
+ − 61 </outputs>
+ − 62 <help>
+ − 63 <![CDATA[
+ − 64 Apply ANCOM to identify features that differ in abundance.
+ − 65 ----------------------------------------------------------
+ − 66
+ − 67 Apply Analysis of Composition of Microbiomes (ANCOM) to identify features
+ − 68 that are differentially abundant across groups.
+ − 69
+ − 70 Parameters
+ − 71 ----------
+ − 72 table : FeatureTable[Composition]
+ − 73 The feature table to be used for ANCOM computation.
+ − 74 metadata : MetadataColumn[Categorical]
+ − 75 The categorical sample metadata column to test for differential
+ − 76 abundance across.
+ − 77 transform_function : Str % Choices({'clr', 'log', 'sqrt'}), optional
+ − 78 The method applied to transform feature values before generating
+ − 79 volcano plots.
+ − 80 difference_function : Str % Choices({'f_statistic', 'mean_difference'}), optional
+ − 81 The method applied to visualize fold difference in feature abundances
+ − 82 across groups for volcano plots.
+ − 83
+ − 84 Returns
+ − 85 -------
+ − 86 visualization : Visualization
+ − 87
+ − 88 ]]>
+ − 89 </help>
+ − 90 <macros>
+ − 91 <import>qiime_citation.xml</import>
+ − 92 </macros>
+ − 93 <expand macro="qiime_citation" />
+ − 94 </tool>
