comparison qiime2-2020.8/qiime_demux_summarize.xml @ 20:d93d8888f0b0 draft

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20:d93d8888f0b0

<?xml version="1.0" ?>
<tool id="qiime_demux_summarize" name="qiime demux summarize"
      version="2020.8">
  <description>Summarize counts per sample.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime demux summarize
# 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

--p-n=$pn

--o-visualization=ovisualization

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

;
cp osubsampledsequences.qza $osubsampledsequences

;
qiime tools export  ovisualization.qzv --output-path out
&& mkdir -p '$ovisualization.files_path'
&& cp -r out/* '$ovisualization.files_path'
&& mv '$ovisualization.files_path/index.html' '$ovisualization'

  ]]></command>
  <inputs>
    <repeat name="input_files_idata" optional="False" title="--i-data">
      <param format="qza,no_unzip.zip" label="--i-data: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality] The demultiplexed sequences to be summarized. [required]" name="additional_input" optional="False" type="data" />
    </repeat>
    <param label="--p-n: INTEGER        The number of sequences that should be selected at random for quality score plots. The quality plots will present the average positional qualities across all of the sequences selected. If input sequences are paired end, plots will be generated for both forward and reverse reads for the same `n` sequences. [default: 10000]" name="pn" optional="True" type="integer" value="10000" />
    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
    
  </inputs>

  <outputs>
    <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
    
  </outputs>

  <help><![CDATA[
Summarize counts per sample.
###############################################################

Summarize counts per sample for all samples, and generate interactive
positional quality plots based on `n` randomly selected sequences.

Parameters
----------
data : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]
    The demultiplexed sequences to be summarized.
n : Int, optional
    The number of sequences that should be selected at random for quality
    score plots. The quality plots will present the average positional
    qualities across all of the sequences selected. If input sequences are
    paired end, plots will be generated for both forward and reverse reads
    for the same `n` sequences.

Returns
-------
visualization : Visualization
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>