comparison fastq_to_tabular.xml @ 1:81c9b58760ff draft

planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

0:e018cfd2dc02

    <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
  </requirements>
  <command interpreter="python">fastq_to_tabular.py '$input_file' '$output_file' $descr_columns '${input_file.extension[len( 'fastq' ):]}'</command>
  <inputs>
    <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqillumina,fastqsolexa" label="FASTQ file to convert" />
    <param name="descr_columns" type="integer" size="2" value="1" label="How many columns to divide title string into?" help="Typically 2 to take the ID (first word) and decription (rest) as two columns, or 1 to give a single column">
      <validator type="in_range" min="1" />
    </param>
  </inputs>
  <outputs>
    <data name="output_file" format="tabular" />

Note the sequences and quality strings have been truncated for display purposes in the above tables.

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**Citation**

If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_


  </help>
</tool>

1:81c9b58760ff

    <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
  </requirements>
  <command interpreter="python">fastq_to_tabular.py '$input_file' '$output_file' $descr_columns '${input_file.extension[len( 'fastq' ):]}'</command>
  <inputs>
    <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqillumina,fastqsolexa" label="FASTQ file to convert" />
    <param name="descr_columns" type="integer" value="1" label="How many columns to divide title string into?" help="Typically 2 to take the ID (first word) and decription (rest) as two columns, or 1 to give a single column">
      <validator type="in_range" min="1" />
    </param>
  </inputs>
  <outputs>
    <data name="output_file" format="tabular" />

Note the sequences and quality strings have been truncated for display purposes in the above tables.

------

  </help>
  
  <citations>
    <citation type="doi">10.1093/bioinformatics/btq281</citation>
  </citations>
  
</tool>