comparison qiime2-2020.8/qiime_composition_ancom.xml @ 20:d93d8888f0b0 draft

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20:d93d8888f0b0

<?xml version="1.0" ?>
<tool id="qiime_composition_ancom" name="qiime composition ancom"
      version="2020.8">
  <description>Apply ANCOM to identify features that differ in abundance.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime composition ancom

--i-table=$itable
# 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($ptransformfunction) != 'None':
--p-transform-function=$ptransformfunction
#end if

#if str($pdifferencefunction) != 'None':
--p-difference-function=$pdifferencefunction
#end if

--o-visualization=ovisualization

#if str($examples) != 'None':
--examples=$examples
#end if

;
cp ocompositiontable.qza $ocompositiontable

;
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-table: ARTIFACT FeatureTable[Composition] The feature table to be used for ANCOM computation. [required]" name="itable" 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[Categorical] The categorical sample metadata column to test for differential abundance across.               [required]" name="mmetadatacolumn" optional="False" type="text" />
    <param label="--p-transform-function: " name="ptransformfunction" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="sqrt">sqrt</option>
      <option value="log">log</option>
      <option value="clr">clr</option>
    </param>
    <param label="--p-difference-function: " name="pdifferencefunction" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="mean_difference">mean_difference</option>
      <option value="f_statistic">f_statistic</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[
Apply ANCOM to identify features that differ in abundance.
###############################################################

Apply Analysis of Composition of Microbiomes (ANCOM) to identify features
that are differentially abundant across groups.

Parameters
----------
table : FeatureTable[Composition]
    The feature table to be used for ANCOM computation.
metadata : MetadataColumn[Categorical]
    The categorical sample metadata column to test for differential
    abundance across.
transform_function : Str % Choices('sqrt', 'log', 'clr'), optional
    The method applied to transform feature values before generating
    volcano plots.
difference_function : Str % Choices('mean_difference', 'f_statistic'), optional
    The method applied to visualize fold difference in feature abundances
    across groups for volcano plots.

Returns
-------
visualization : Visualization
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>