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+ − 1 <?xml version="1.0" ?>
+ − 2 <tool id="qiime_emperor_plot" name="qiime emperor plot" version="2018.4">
+ − 3 <description> - Visualize and Interact with Principal Coordinates Analysis Plots</description>
+ − 4 <requirements>
+ − 5 <requirement type="package" version="2018.4">qiime2</requirement>
+ − 6 </requirements>
+ − 7 <command><![CDATA[
+ − 8 qiime emperor plot
+ − 9
+ − 10 #def list_dict_to_string(list_dict):
+ − 11 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
+ − 12 #for d in list_dict[1:]:
+ − 13 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
+ − 14 #end for
+ − 15 #return $file_list
+ − 16 #end def
+ − 17
+ − 18 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --i-pcoa=$ipcoa
+ − 19
+ − 20 #if str($cmdconfig) != 'None':
+ − 21 --cmd-config=$cmdconfig
+ − 22 #end if
+ − 23
+ − 24 #if str($pcustomaxes):
+ − 25 --p-custom-axes="$pcustomaxes"
+ − 26 #end if
+ − 27
+ − 28 --o-visualization=ovisualization;
+ − 29
+ − 30 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
+ − 31 && cp -r out/* '$ovisualization.files_path'
+ − 32 && mv '$ovisualization.files_path/index.html' '$ovisualization';
+ − 33 ]]></command>
+ − 34 <inputs>
+ − 35 <param format="qza,no_unzip.zip" label="--i-pcoa: PCoAResults The principal coordinates matrix to be plotted. [required]" name="ipcoa" optional="False" type="data"/>
+ − 36 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
+ − 37 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The sample metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
+ − 38 </repeat>
+ − 39 <param label="--p-custom-axes: Numeric sample metadata columns that should be included as axes in the Emperor plot. [optional]" name="pcustomaxes" optional="True" type="text"/>
+ − 40 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
+ − 41 </inputs>
+ − 42 <outputs>
+ − 43 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
+ − 44 </outputs>
+ − 45 <help><![CDATA[
+ − 46 Visualize and Interact with Principal Coordinates Analysis Plots
+ − 47 ----------------------------------------------------------------
+ − 48
+ − 49 Generate visualization of your ordination.
+ − 50
+ − 51 Parameters
+ − 52 ----------
+ − 53 pcoa : PCoAResults
+ − 54 The principal coordinates matrix to be plotted.
+ − 55 metadata : Metadata
+ − 56 The sample metadata.
+ − 57 custom_axes : List[Str], optional
+ − 58 Numeric sample metadata columns that should be included as axes in the
+ − 59 Emperor plot.
+ − 60
+ − 61 Returns
+ − 62 -------
+ − 63 visualization : Visualization
+ − 64 \
+ − 65 ]]>
+ − 66 </help>
+ − 67 <macros>
+ − 68 <import>qiime_citation.xml</import>
+ − 69 </macros>
+ − 70 <expand macro="qiime_citation" />
+ − 71 </tool>
