annotate qiime2-2020.8/qiime_feature-table_filter-seqs.xml @ 20:d93d8888f0b0 draft

Uploaded

<?xml version="1.0" ?>
<tool id="qiime_feature-table_filter-seqs" name="qiime feature-table filter-seqs"
      version="2020.8">
  <description>Filter features from sequences</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime feature-table filter-seqs
# if $input_files_idata:
  # 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 + ' --i-data=' + d['additional_input'].__getattr__('file_name')
    # end for
    # return $file_list
  # end def
--i-data=$list_dict_to_string($input_files_idata)
# end if

#if str($itable) != 'None':
--i-table=$itable
#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-data=ofiltereddata

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

;
cp ofiltereddata.qza $ofiltereddata

  ]]></command>
  <inputs>
    <repeat name="input_files_idata" optional="False" title="--i-data">
      <param format="qza,no_unzip.zip" label="--i-data: ARTIFACT FeatureData[Sequence¹ | AlignedSequence²] The sequences from which features should be filtered. [required]" name="additional_input" optional="False" type="data" />
    </repeat>
    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Table containing feature ids used for id-based filtering.                                   [optional]" 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... (multiple          Feature metadata used for id-based filtering, with arguments will    `where` parameter when selecting features to retain, or be merged)        with `exclude-ids` 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 sequences 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 the `metadata` (with or without the `where` parameter) or `table` parameter will be excluded from the filtered sequences 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}: filtereddata.qza" name="ofiltereddata" />
    
  </outputs>

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

Filter features from sequences based on a feature table or metadata. See
the filtering tutorial on https://docs.qiime2.org for additional details.
This method can filter based on ids in a table or a metadata file, but not
both (i.e., the table and metadata options are mutually exclusive).

Parameters
----------
data : FeatureData[Sequence¹ | AlignedSequence²]
    The sequences from which features should be filtered.
table : FeatureTable[Frequency], optional
    Table containing feature ids used for id-based filtering.
metadata : Metadata, optional
    Feature metadata used for id-based filtering, 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 sequences will be retained.
exclude_ids : Bool, optional
    If true, the features selected by the `metadata` (with or without the
    `where` parameter) or `table` parameter will be excluded from the
    filtered sequences instead of being retained.

Returns
-------
filtered_data : FeatureData[Sequence¹ | AlignedSequence²]
    The resulting filtered sequences.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>