comparison qiime2/qiime_longitudinal_anova.xml @ 14:a0a8d77a991c draft

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13:887cd4ad8e16

<?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[
qiime longitudinal anova




#if 'X' in str($pformula):
  #set $pformula_temp = $pformula.replace('X', "~")
  #set $pformula = $pformula_temp
#end if

--p-formula="$pformula"



#if str($psstype) != 'None':
 --p-sstype=$psstype
#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)
#end if


--o-visualization=ovisualization
;
qiime tools export --input-path 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>

		<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="html" label="${tool.name} on ${on_string}: visualization.qzv" 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.

    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>

14:a0a8d77a991c

<?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.

    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>