Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2-2020.8/qiime_diversity_beta-correlation.xml @ 20:d93d8888f0b0 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 12:44:24 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2-2020.8/qiime_diversity_beta-correlation.xml Fri Sep 04 12:44:24 2020 +0000 @@ -0,0 +1,160 @@ +<?xml version="1.0" ?> +<tool id="qiime_diversity_beta-correlation" name="qiime diversity beta-correlation" + version="2020.8"> + <description>Beta diversity correlation</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime diversity beta-correlation + +--i-distance-matrix=$idistancematrix +# 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($input_files_mmetadatafile) +# end if + +#if '__ob__' in str($mmetadatacolumn): + #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__ob__', '[') + #set $mmetadatacolumn = $mmetadatacolumn_temp +#end if +#if '__cb__' in str($mmetadatacolumn): + #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__cb__', ']') + #set $mmetadatacolumn = $mmetadatacolumn_temp +#end if +#if 'X' in str($mmetadatacolumn): + #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('X', '\\') + #set $mmetadatacolumn = $mmetadatacolumn_temp +#end if +#if '__sq__' in str($mmetadatacolumn): + #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'") + #set $mmetadatacolumn = $mmetadatacolumn_temp +#end if +#if '__db__' in str($mmetadatacolumn): + #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__db__', '"') + #set $mmetadatacolumn = $mmetadatacolumn_temp +#end if + +--m-metadata-column=$mmetadatacolumn + + +#if str($pmethod) != 'None': +--p-method=$pmethod +#end if + +--p-permutations=$ppermutations + +#if $pintersectids: + --p-intersect-ids +#end if + +#if str($plabel1): + --p-label1=$plabel1 +#end if +#if str($plabel2): + --p-label2=$plabel2 +#end if# if $input_files_ometadatadistancematrix: + # 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 + ' --o-metadata-distance-matrix=' + d['additional_input'].__getattr__('file_name') + # end for + # return $file_list + # end def +--o-metadata-distance-matrix=$list_dict_to_string($input_files_ometadatadistancematrix) +# end if + +--o-mantel-scatter-visualization=omantelscattervisualization + +#if str($examples) != 'None': +--examples=$examples +#end if + +; +cp odistancematrix.qza $odistancematrix + +; +qiime tools export omantelscattervisualization.qzv --output-path out +&& mkdir -p '$omantelscattervisualization.files_path' +&& cp -r out/* '$omantelscattervisualization.files_path' +&& mv '$omantelscattervisualization.files_path/index.html' '$omantelscattervisualization' + + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data" /> + <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> + <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" /> + </repeat> + <param label="--m-metadata-column: COLUMN MetadataColumn[Numeric] Numeric metadata column from which to compute pairwise Euclidean distances [required]" name="mmetadatacolumn" optional="False" type="text" /> + <param label="--p-method: " name="pmethod" optional="True" type="select"> + <option selected="True" value="None">Selection is Optional</option> + <option value="spearman">spearman</option> + <option value="pearson">pearson</option> + </param> + <param label="--p-permutations: INTEGER Range(0, None) The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]" min="0" name="ppermutations" optional="True" type="integer" value="999" /> + <param label="--p-intersect-ids: --p-intersect-ids: / --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]" name="pintersectids" selected="False" type="boolean" /> + <param label="--p-label1: TEXT Label for `distance-matrix` in the output visualization. [default: \'Metadata\']" name="plabel1" optional="False" type="text" value="\'Metadata\'" /> + <param label="--p-label2: TEXT Label for `metadata-distance-matrix` in the output visualization. [default: \'Distance Matrix\']" name="plabel2" optional="False" type="text" value="\'Distance Matrix\'" /> + <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> + + </inputs> + + <outputs> + <repeat name="input_files_ometadatadistancematrix" optional="False" title="--o-metadata-distance-matrix"> + <param format="tabular,qza,no_unzip.zip" label="--o-metadata-distance-matrix: ARTIFACT DistanceMatrix The Distance Matrix produced from the metadata column and used in the mantel test [required]" name="additional_input" optional="False" type="data" /> + </repeat> + <data format="html" label="${tool.name} on ${on_string}: mantelscattervisualization.html" name="omantelscattervisualization" /> + + </outputs> + + <help><![CDATA[ +Beta diversity correlation +############################################################### + +Create a distance matrix from a numeric metadata column and apply a two- +sided Mantel test to identify correlation between two distance matrices. +Actions used internally: `distance-matrix` from q2-metadata and `mantel` +from q2-diversity. + +Parameters +---------- +metadata : MetadataColumn[Numeric] + Numeric metadata column from which to compute pairwise Euclidean + distances +distance_matrix : DistanceMatrix + Matrix of distances between pairs of samples. +method : Str % Choices('spearman', 'pearson'), optional + The correlation test to be applied in the Mantel test. +permutations : Int % Range(0, None), optional + The number of permutations to be run when computing p-values. Supplying + a value of zero will disable permutation testing and p-values will not + be calculated (this results in *much* quicker execution time if + p-values are not desired). +intersect_ids : Bool, optional + If supplied, IDs that are not found in both distance matrices will be + discarded before applying the Mantel test. Default behavior is to error + on any mismatched IDs. +label1 : Str, optional + Label for `distance_matrix` in the output visualization. +label2 : Str, optional + Label for `metadata_distance_matrix` in the output visualization. + +Returns +------- +metadata_distance_matrix : DistanceMatrix + The Distance Matrix produced from the metadata column and used in the + mantel test +mantel_scatter_visualization : Visualization + Scatter plot rendering of the manteltest results + ]]></help> + <macros> + <import>qiime_citation.xml</import> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file