Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_metadata_distance-matrix.xml @ 0:370e0b6e9826 draft
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author | florianbegusch |
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date | Wed, 17 Jul 2019 03:05:17 -0400 |
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children | f190567fe3f6 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_metadata_distance-matrix.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,62 @@ +<?xml version="1.0" ?> +<tool id="qiime_metadata_distance-matrix" name="qiime metadata distance-matrix" version="2019.4"> + <description> - Create a distance matrix from a numeric Metadata column</description> + <requirements> + <requirement type="package" version="2019.4">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime metadata distance-matrix + +--m-metadata-column="$mmetadatacolumn" + + +#if $input_files_mmetadatafile: +#def list_dict_to_string(list_dict): + #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') + #for d in list_dict[1:]: + #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name') + #end for + #return $file_list +#end def + --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) +#end if + + +--o-distance-matrix=odistancematrix +; +cp odistancematrix.qza $odistancematrix + ]]></command> + <inputs> + <param label="--m-metadata-column: COLUMN MetadataColumn[Numeric] Numeric metadata column to compute pairwise Euclidean distances from [required]" name="mmetadatacolumn" optional="False" type="text"/> + + <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> + <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> + </repeat> + + </inputs> + <outputs> + <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix"/> + </outputs> + <help><![CDATA[ +Create a distance matrix from a numeric Metadata column +####################################################### + +Create a distance matrix from a numeric metadata column. The Euclidean +distance is computed between each pair of samples or features in the +column. Tip: the distance matrix produced by this method can be used as +input to the Mantel test available in `q2-diversity`. + +Parameters +---------- +metadata : MetadataColumn[Numeric] + Numeric metadata column to compute pairwise Euclidean distances from + +Returns +------- +distance_matrix : DistanceMatrix + ]]></help> +<macros> + <import>qiime_citation.xml</import> +</macros> +<expand macro="qiime_citation"/> +</tool>