annotate qiime2/qiime_feature-table_filter-features.xml @ 15:276ec629f09a draft

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<?xml version="1.0" ?>
<tool id="qiime_feature-table_filter-features" name="qiime feature-table filter-features"
      version="2020.8">
  <description>Filter features from table</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime feature-table filter-features

--i-table=$itable

--p-min-frequency=$pminfrequency

#if str($pmaxfrequency):
  --p-max-frequency=$pmaxfrequency
#end if
--p-min-samples=$pminsamples

#if str($pmaxsamples):
  --p-max-samples=$pmaxsamples
#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

#if '__ob__' in str($pwhere):
  #set $pwhere_temp = $pwhere.replace('__ob__', '[')
  #set $pwhere = $pwhere_temp
#end if
#if '__cb__' in str($pwhere):
  #set $pwhere_temp = $pwhere.replace('__cb__', ']')
  #set $pwhere = $pwhere_temp
#end if
#if 'X' in str($pwhere):
  #set $pwhere_temp = $pwhere.replace('X', '\\')
  #set $pwhere = $pwhere_temp
#end if
#if '__sq__' in str($pwhere):
  #set $pwhere_temp = $pwhere.replace('__sq__', "'")
  #set $pwhere = $pwhere_temp
#end if
#if '__db__' in str($pwhere):
  #set $pwhere_temp = $pwhere.replace('__db__', '"')
  #set $pwhere = $pwhere_temp
#end if

#if str($pwhere):
  --p-where=$pwhere
#end if

#if $pexcludeids:
 --p-exclude-ids
#end if

--o-filtered-table=ofilteredtable

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

;
cp ofilteredtable.qza $ofilteredtable

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table from which features should be filtered.                                    [required]" name="itable" optional="False" type="data" />
    <param label="--p-min-frequency: INTEGER The minimum total frequency that a feature must have to be retained.                            [default: 0]" name="pminfrequency" optional="True" type="integer" value="0" />
    <param label="--p-max-frequency: INTEGER The maximum total frequency that a feature can have to be retained. If no value is provided this will default to infinity (i.e., no maximum frequency filter will be applied).                                    [optional]" name="pmaxfrequency" optional="False" type="text" />
    <param label="--p-min-samples: INTEGER The minimum number of samples that a feature must be observed in to be retained.                [default: 0]" name="pminsamples" optional="True" type="integer" value="0" />
    <param label="--p-max-samples: INTEGER The maximum number of samples that a feature can be observed in to be retained. If no value is provided this will default to infinity (i.e., no maximum sample filter will be applied).                     [optional]" name="pmaxsamples" optional="False" type="text" />
    <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple          Feature metadata used with `where` parameter when arguments will    selecting features to retain, or with `exclude-ids` be merged)        when selecting features to discard.          [optional]" name="additional_input" optional="True" type="data" />
    </repeat>
    <param label="--p-where: TEXT       SQLite WHERE clause specifying feature metadata criteria that must be met to be included in the filtered feature table. If not provided, all features in `metadata` that are also in the feature table will be retained.                                 [optional]" name="pwhere" optional="False" type="text" />
    <param label="--p-exclude-ids: --p-exclude-ids: / --p-no-exclude-ids If true, the features selected by `metadata` or `where` parameters will be excluded from the filtered table instead of being retained.       [default: False]" name="pexcludeids" selected="False" type="boolean" />
    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
    
  </inputs>

  <outputs>
    <data format="qza" label="${tool.name} on ${on_string}: filteredtable.qza" name="ofilteredtable" />
    
  </outputs>

  <help><![CDATA[
Filter features from table
###############################################################

Filter features from table based on frequency and/or metadata. Any samples
with a frequency of zero after feature filtering will also be removed. See
the filtering tutorial on https://docs.qiime2.org for additional details.

Parameters
----------
table : FeatureTable[Frequency]
    The feature table from which features should be filtered.
min_frequency : Int, optional
    The minimum total frequency that a feature must have to be retained.
max_frequency : Int, optional
    The maximum total frequency that a feature can have to be retained. If
    no value is provided this will default to infinity (i.e., no maximum
    frequency filter will be applied).
min_samples : Int, optional
    The minimum number of samples that a feature must be observed in to be
    retained.
max_samples : Int, optional
    The maximum number of samples that a feature can be observed in to be
    retained. If no value is provided this will default to infinity (i.e.,
    no maximum sample filter will be applied).
metadata : Metadata, optional
    Feature metadata used with `where` parameter when selecting features to
    retain, or with `exclude_ids` when selecting features to discard.
where : Str, optional
    SQLite WHERE clause specifying feature metadata criteria that must be
    met to be included in the filtered feature table. If not provided, all
    features in `metadata` that are also in the feature table will be
    retained.
exclude_ids : Bool, optional
    If true, the features selected by `metadata` or `where` parameters will
    be excluded from the filtered table instead of being retained.

Returns
-------
filtered_table : FeatureTable[Frequency]
    The resulting feature table filtered by feature.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>