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1 <tool id="tabular_to_fastq" name="Tabular to FASTQ" version="1.0.0">
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2 <description>converter</description>
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3 <command interpreter="python">tabular_to_fastq.py '$input_file' '$output_file' '$identifier' '$sequence' '$quality'</command>
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4 <inputs>
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5 <param name="input_file" type="data" format="tabular" label="Tabular file to convert" />
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6 <param name="identifier" label="Identifier column" type="data_column" data_ref="input_file" />
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7 <param name="sequence" label="Sequence column" type="data_column" data_ref="input_file" />
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8 <param name="quality" label="Quality column" type="data_column" data_ref="input_file" />
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9 </inputs>
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10 <outputs>
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11 <data name="output_file" format="fastq" />
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12 </outputs>
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13 <tests>
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14 <!-- basic test -->
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15 <test>
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16 <param name="input_file" value="fastq_to_tabular_out_1.tabular" ftype="tabular" />
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17 <param name="identifier" value="1" />
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18 <param name="sequence" value="2" />
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19 <param name="quality" value="3" />
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20 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
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21 </test>
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22 <!-- color space test -->
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23 <test>
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24 <param name="input_file" value="fastq_to_tabular_out_2.tabular" ftype="tabular" />
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25 <param name="identifier" value="1" />
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26 <param name="sequence" value="2" />
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27 <param name="quality" value="3" />
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28 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
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29 </test>
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30 </tests>
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31 <help>
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32 **What it does**
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33
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34 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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35
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36 ------
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37
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38 **Citation**
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39
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40 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>`_
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41
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42
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43 </help>
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44 </tool>
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