Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2-2020.8/qiime_longitudinal_anova.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_longitudinal_anova.xml Fri Sep 04 12:44:24 2020 +0000 @@ -0,0 +1,100 @@ +<?xml version="1.0" ?> +<tool id="qiime_longitudinal_anova" name="qiime longitudinal anova" + version="2020.8"> + <description>ANOVA test</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime longitudinal anova +# 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 $pformula: + --p-formula +#end if + +#if str($psstype) != 'None': +--p-sstype=$psstype +#end if + +--o-visualization=ovisualization + +#if str($examples) != 'None': +--examples=$examples +#end if + +; +cp ohierarchy.qza $ohierarchy + +; +qiime tools export ovisualization.qzv --output-path out +&& mkdir -p '$ovisualization.files_path' +&& cp -r out/* '$ovisualization.files_path' +&& mv '$ovisualization.files_path/index.html' '$ovisualization' + + ]]></command> + <inputs> + <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> + <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Sample metadata containing formula terms. arguments will be merged) [required]" name="additional_input" optional="False" type="data" /> + </repeat> + <param label="--p-formula: --p-formula: TEXT R-style formula specifying the model. All terms must be present in the sample metadata or metadata-transformable artifacts and can be continuous or categorical metadata columns. Formulae will be in the format \'a ~ b + c\', where \'a\' is the metric (dependent variable) and \'b\' and \'c\' are independent covariates. Use \'+\' to add a variable; \'+ a:b\' to add an interaction between variables a and b; \'*\' to include a variable and all interactions; and \'-\' to subtract a particular term (e.g., an interaction term). See https://patsy.readthedocs.io/en/latest/formulas.html for full documentation of valid formula operators. Always enclose formulae in quotes to avoid unpleasant surprises. [required]" name="pformula" selected="False" type="boolean" /> + <param label="--p-sstype: " name="psstype" optional="True" type="select"> + <option selected="True" value="None">Selection is Optional</option> + <option value="I">I</option> + <option value="II">II</option> + <option value="III">III</option> + </param> + <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> + + </inputs> + + <outputs> + <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" /> + + </outputs> + + <help><![CDATA[ +ANOVA test +############################################################### + +Perform an ANOVA test on any factors present in a metadata file and/or +metadata-transformable artifacts. This is followed by pairwise t-tests to +examine pairwise differences between categorical sample groups. + +Parameters +---------- +metadata : Metadata + Sample metadata containing formula terms. +formula : Str + R-style formula specifying the model. All terms must be present in the + sample metadata or metadata-transformable artifacts and can be + continuous or categorical metadata columns. Formulae will be in the + format "a ~ b + c", where "a" is the metric (dependent variable) and + "b" and "c" are independent covariates. Use "+" to add a variable; "+ + a:b" to add an interaction between variables a and b; "*" to include a + variable and all interactions; and "-" to subtract a particular term + (e.g., an interaction term). See + https://patsy.readthedocs.io/en/latest/formulas.html for full + documentation of valid formula operators. Always enclose formulae in + quotes to avoid unpleasant surprises. +sstype : Str % Choices('I', 'II', 'III'), optional + Type of sum of squares calculation to perform (I, II, or III). + +Returns +------- +visualization : Visualization + ]]></help> + <macros> + <import>qiime_citation.xml</import> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file