annotate qiime2/qiime_demux_filter-samples.xml @ 29:3ba9833030c1 draft

Uploaded

<?xml version="1.0" ?>
<tool id="qiime_demux_filter-samples" name="qiime demux filter-samples"
      version="2020.8">
  <description>Filter samples out of demultiplexed data.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime demux filter-samples

--i-demux=$idemux
# 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-demux=ofiltereddemux

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

;
cp ofiltereddemux.qza $ofiltereddemux

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-demux: ARTIFACT SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³] The demultiplexed data from which samples should be filtered.                                    [required]" name="idemux" optional="False" type="data" />
    <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 indicating which sample ids to filter. arguments will    The optional `where` parameter may be used to filter be merged)        ids based on specified conditions in the metadata. The optional `exclude-ids` parameter may be used to exclude the ids specified in the metadata from the filter. [required]" name="additional_input" optional="False" type="data" />
    </repeat>
    <param label="--p-where: TEXT       Optional SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered data. If not provided, all samples in `metadata` that are also in the demultiplexed data will be retained.                                 [optional]" name="pwhere" optional="False" type="text" />
    <param label="--p-exclude-ids: --p-exclude-ids: / --p-no-exclude-ids Defaults to False. If True, the samples selected by the `metadata` and optional `where` parameter will be excluded from the filtered data.       [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}: filtereddemux.qza" name="ofiltereddemux" />
    
  </outputs>

  <help><![CDATA[
Filter samples out of demultiplexed data.
###############################################################

Filter samples indicated in given metadata out of demultiplexed data.
Specific samples can be further selected with the WHERE clause, and the
`exclude_ids` parameter allows for filtering of all samples not specified.

Parameters
----------
demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]
    The demultiplexed data from which samples should be filtered.
metadata : Metadata
    Sample metadata indicating which sample ids to filter. The optional
    `where` parameter may be used to filter ids based on specified
    conditions in the metadata. The optional `exclude_ids` parameter may be
    used to exclude the ids specified in the metadata from the filter.
where : Str, optional
    Optional SQLite WHERE clause specifying sample metadata criteria that
    must be met to be included in the filtered data. If not provided, all
    samples in `metadata` that are also in the demultiplexed data will be
    retained.
exclude_ids : Bool, optional
    Defaults to False. If True, the samples selected by the `metadata` and
    optional `where` parameter will be excluded from the filtered data.

Returns
-------
filtered_demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]
    Filtered demultiplexed data.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>