Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_longitudinal_anova.xml @ 14:a0a8d77a991c draft
Uploaded
author | florianbegusch |
---|---|
date | Thu, 03 Sep 2020 09:51:29 +0000 |
parents | f190567fe3f6 |
children |
line wrap: on
line diff
--- a/qiime2/qiime_longitudinal_anova.xml Thu Sep 03 09:46:00 2020 +0000 +++ b/qiime2/qiime_longitudinal_anova.xml Thu Sep 03 09:51:29 2020 +0000 @@ -1,67 +1,70 @@ <?xml version="1.0" ?> -<tool id="qiime_longitudinal_anova" name="qiime longitudinal anova" version="2019.7"> - <description> - ANOVA test</description> - <requirements> - <requirement type="package" version="2019.7">qiime2</requirement> - </requirements> - <command><![CDATA[ +<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($input_files_mmetadatafile) +# end if -#if 'X' in str($pformula): - #set $pformula_temp = $pformula.replace('X', "~") - #set $pformula = $pformula_temp +#if $pformula: + --p-formula #end if ---p-formula="$pformula" - +#if str($psstype) != 'None': +--p-sstype=$psstype +#end if +--o-visualization=ovisualization -#if str($psstype) != 'None': - --p-sstype=$psstype +#if str($examples) != 'None': +--examples=$examples #end if +; +cp ohierarchy.qza $ohierarchy -#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($input_files_mmetadatafile) -#end if - - ---o-visualization=ovisualization ; -qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' +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 label="--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" optional="False" type="text"/> - <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> +&& mv '$ovisualization.files_path/index.html' '$ovisualization' - <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> + ]]></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> - </inputs> - <outputs> - <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> - </outputs> - <help><![CDATA[ + <outputs> + <data format="html" label="${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 @@ -89,9 +92,9 @@ 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