view tabular_to_fastq.xml @ 0:9ae652b76979 draft

Imported from capsule None

<tool id="tabular_to_fastq" name="Tabular to FASTQ" version="1.0.0">
  <description>converter</description>
  <requirements>
    <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
  </requirements>
  <command interpreter="python">tabular_to_fastq.py '$input_file' '$output_file' '$identifier' '$sequence' '$quality'</command>
  <inputs>
    <param name="input_file" type="data" format="tabular" label="Tabular file to convert" />
    <param name="identifier" label="Identifier column" type="data_column" data_ref="input_file" />
    <param name="sequence" label="Sequence column" type="data_column" data_ref="input_file" />
    <param name="quality" label="Quality column" type="data_column" data_ref="input_file" />
  </inputs>
  <outputs>
    <data name="output_file" format="fastq" />
  </outputs>
  <tests>
    <!-- basic test -->
    <test>
      <param name="input_file" value="fastq_to_tabular_out_1.tabular" ftype="tabular" />
      <param name="identifier" value="1" />
      <param name="sequence" value="2" />
      <param name="quality" value="3" />
      <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
    </test>
    <!-- color space test -->
    <test>
      <param name="input_file" value="fastq_to_tabular_out_2.tabular" ftype="tabular" />
      <param name="identifier" value="1" />
      <param name="sequence" value="2" />
      <param name="quality" value="3" />
      <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
    </test>
  </tests>
  <help>
**What it does**

This tool attempts to convert a tabular file containing sequencing read data to a FASTQ formatted file. The FASTQ Groomer tool should always be used on the output of this tool. 

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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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20562416&gt;`_


  </help>
</tool>