annotate qiime2-2020.8/qiime_feature-table_rename-ids.xml @ 20:d93d8888f0b0 draft

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<?xml version="1.0" ?>
<tool id="qiime_feature-table_rename-ids" name="qiime feature-table rename-ids"
      version="2020.8">
  <description>Renames sample or feature ids in a table</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime feature-table rename-ids

--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($paxis) != 'None':
--p-axis=$paxis
#end if

#if $pstrict:
 --p-strict
#end if

--o-renamed-table=orenamedtable

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

;
cp orenamedtable.qza $orenamedtable

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴] The table to be renamed                      [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] A metadata column defining the new ids. Each original id must map to a new unique id. If strict mode is used, then every id in the original table must have a new id. [required]" name="mmetadatacolumn" optional="False" type="text" />
    <param label="--p-axis: " name="paxis" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="sample">sample</option>
      <option value="feature">feature</option>
    </param>
    <param label="--p-strict: --p-strict: / --p-no-strict Whether the naming needs to be strict (each id in the table must have a new id). Otherwise, only the ids described in `metadata` will be renamed and the others will keep their original id names.     [default: False]" name="pstrict" 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}: renamedtable.qza" name="orenamedtable" />
    
  </outputs>

  <help><![CDATA[
Renames sample or feature ids in a table
###############################################################

Renames the sample or feature ids in a feature table using metadata to
define the new ids.

Parameters
----------
table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]
    The table to be renamed
metadata : MetadataColumn[Categorical]
    A metadata column defining the new ids. Each original id must map to a
    new unique id. If strict mode is used, then every id in the original
    table must have a new id.
axis : Str % Choices('sample', 'feature'), optional
    Along which axis to rename the ids.
strict : Bool, optional
    Whether the naming needs to be strict (each id in the table must have a
    new id). Otherwise, only the ids described in `metadata` will be
    renamed and the others will keep their original id names.

Returns
-------
renamed_table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]
    A table which has new ids, where the ids are replaced by values in the
    `metadata` column.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>