view qiime2-2020.8/qiime_demux_emp-paired.xml @ 20:d93d8888f0b0 draft

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<?xml version="1.0" ?>
<tool id="qiime_demux_emp-paired" name="qiime demux emp-paired"
      version="2020.8">
  <description>Demultiplex paired-end sequence data generated with the EMP protocol.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime demux emp-paired

--i-seqs=$iseqs
# if $input_files_mbarcodesfile:
  # 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-barcodes-file=' + d['additional_input'].__getattr__('file_name')
    # end for
    # return $file_list
  # end def
--m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
# end if

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

--m-barcodes-column=$mbarcodescolumn


#if $pnogolayerrorcorrection:
 --p-no-golay-error-correction
#end if

#if $prevcompbarcodes:
 --p-rev-comp-barcodes
#end if

#if $prevcompmappingbarcodes:
 --p-rev-comp-mapping-barcodes
#end if

--o-per-sample-sequences=opersamplesequences

--o-error-correction-details=oerrorcorrectiondetails

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

;
cp oerrorcorrectiondetails.qza $oerrorcorrectiondetails

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT EMPPairedEndSequences The paired-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data" />
    <repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file">
      <param format="tabular,qza,no_unzip.zip" label="--m-barcodes-file: METADATA" name="additional_input" optional="True" type="data" />
    </repeat>
    <param label="--m-barcodes-column: COLUMN  MetadataColumn[Categorical] The sample metadata column containing the per-sample barcodes.                                    [required]" name="mbarcodescolumn" optional="False" type="text" />
    <param label="--p-no-golay-error-correction: Do not perform 12nt Golay error correction on the barcode reads.                                  [default: True]" name="pnogolayerrorcorrection" selected="False" type="boolean" />
    <param format="tabular,qza,no_unzip.zip" label="--p-rev-comp-barcodes: --p-rev-comp-barcodes: / --p-no-rev-comp-barcodes If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompbarcodes" selected="False" type="boolean" />
    <param format="tabular,qza,no_unzip.zip" label="--p-rev-comp-mapping-barcodes: --p-rev-comp-mapping-barcodes: / --p-no-rev-comp-mapping-barcodes If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing.                        [default: False]" name="prevcompmappingbarcodes" 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 ${on_string}: persamplesequences.qza" name="opersamplesequences" />
    <data format="qza" label="${tool.name} on ${on_string}: errorcorrectiondetails.qza" name="oerrorcorrectiondetails" />
    
  </outputs>

  <help><![CDATA[
Demultiplex paired-end sequence data generated with the EMP protocol.
###############################################################

Demultiplex paired-end sequence data (i.e., map barcode reads to sample
ids) for data generated with the Earth Microbiome Project (EMP) amplicon
sequencing protocol. Details about this protocol can be found at
http://www.earthmicrobiome.org/protocols-and-standards/

Parameters
----------
seqs : EMPPairedEndSequences
    The paired-end sequences to be demultiplexed.
barcodes : MetadataColumn[Categorical]
    The sample metadata column containing the per-sample barcodes.
golay_error_correction : Bool, optional
    Perform 12nt Golay error correction on the barcode reads.
rev_comp_barcodes : Bool, optional
    If provided, the barcode sequence reads will be reverse complemented
    prior to demultiplexing.
rev_comp_mapping_barcodes : Bool, optional
    If provided, the barcode sequences in the sample metadata will be
    reverse complemented prior to demultiplexing.

Returns
-------
per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
    The resulting demultiplexed sequences.
error_correction_details : ErrorCorrectionDetails
    Detail about the barcode error corrections.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>