Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_diversity_alpha-correlation.xml @ 14:a0a8d77a991c draft
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author | florianbegusch |
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date | Thu, 03 Sep 2020 09:51:29 +0000 |
parents | f190567fe3f6 |
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--- a/qiime2/qiime_diversity_alpha-correlation.xml Thu Sep 03 09:46:00 2020 +0000 +++ b/qiime2/qiime_diversity_alpha-correlation.xml Thu Sep 03 09:51:29 2020 +0000 @@ -1,53 +1,72 @@ <?xml version="1.0" ?> -<tool id="qiime_diversity_alpha-correlation" name="qiime diversity alpha-correlation" version="2019.7"> - <description> - Alpha diversity correlation</description> - <requirements> - <requirement type="package" version="2019.7">qiime2</requirement> - </requirements> - <command><![CDATA[ +<tool id="qiime_diversity_alpha-correlation" name="qiime diversity alpha-correlation" + version="2020.8"> + <description>Alpha diversity correlation</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ qiime diversity alpha-correlation --i-alpha-diversity=$ialphadiversity +# 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 $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($input_files_mmetadatafile) +#if str($pmethod) != 'None': +--p-method=$pmethod #end if -#if str($pmethod) != 'None': - --p-method=$pmethod +#if $pintersectids: + --p-intersect-ids #end if --o-visualization=ovisualization + +#if str($examples) != 'None': +--examples=$examples +#end if + ; -qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' +cp oalphadiversity.qza $oalphadiversity + +; +qiime tools export ovisualization.qzv --output-path out +&& mkdir -p '$ovisualization.files_path' && cp -r out/* '$ovisualization.files_path' && mv '$ovisualization.files_path/index.html' '$ovisualization' - ]]></command> - <inputs> - <param format="qza,no_unzip.zip" label="--i-alpha-diversity: ARTIFACT SampleData[AlphaDiversity] Vector of alpha diversity values by sample. [required]" name="ialphadiversity" optional="False" type="data"/> - <param label="--p-method: " name="pmethod" optional="True" type="select"> - <option selected="True" value="None">Selection is Optional</option> - <option value="spearman">spearman</option> - <option value="pearson">pearson</option> - </param> - <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]"> - <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> - </repeat> - </inputs> - <outputs> - <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> - </outputs> - <help><![CDATA[ + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-alpha-diversity: ARTIFACT SampleData[AlphaDiversity] Vector of alpha diversity values by sample. [required]" name="ialphadiversity" optional="False" type="data" /> + <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> + <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple The sample metadata. arguments will be merged) [required]" name="additional_input" optional="False" type="data" /> + </repeat> + <param label="--p-method: " name="pmethod" optional="True" type="select"> + <option selected="True" value="None">Selection is Optional</option> + <option value="spearman">spearman</option> + <option value="pearson">pearson</option> + </param> + <param label="--p-intersect-ids: --p-intersect-ids: / --p-no-intersect-ids If supplied, IDs that are not found in both the alpha diversity vector and metadata will be discarded before calculating the correlation. Default behavior is to error on any mismatched IDs. [default: False]" name="pintersectids" selected="False" type="boolean" /> + <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> + + </inputs> + + <outputs> + <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" /> + + </outputs> + + <help><![CDATA[ Alpha diversity correlation -########################### +############################################################### Determine whether numeric sample metadata columns are correlated with alpha diversity. @@ -60,13 +79,17 @@ The sample metadata. method : Str % Choices('spearman', 'pearson'), optional The correlation test to be applied. +intersect_ids : Bool, optional + If supplied, IDs that are not found in both the alpha diversity vector + and metadata will be discarded before calculating the correlation. + Default behavior is to error on any mismatched IDs. Returns ------- visualization : Visualization - ]]></help> -<macros> + ]]></help> + <macros> <import>qiime_citation.xml</import> -</macros> -<expand macro="qiime_citation"/> -</tool> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file