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annotate tabular_to_fastq.xml @ 0:9ae652b76979 draft

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author devteam
date Thu, 23 Jan 2014 12:31:40 -0500
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children 7bde4f066435
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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 <requirements>
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4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
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5 </requirements>
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6 <command interpreter="python">tabular_to_fastq.py '$input_file' '$output_file' '$identifier' '$sequence' '$quality'</command>
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7 <inputs>
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8 <param name="input_file" type="data" format="tabular" label="Tabular file to convert" />
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9 <param name="identifier" label="Identifier column" type="data_column" data_ref="input_file" />
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10 <param name="sequence" label="Sequence column" type="data_column" data_ref="input_file" />
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11 <param name="quality" label="Quality column" type="data_column" data_ref="input_file" />
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12 </inputs>
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13 <outputs>
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14 <data name="output_file" format="fastq" />
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15 </outputs>
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16 <tests>
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17 <!-- basic test -->
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18 <test>
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19 <param name="input_file" value="fastq_to_tabular_out_1.tabular" ftype="tabular" />
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20 <param name="identifier" value="1" />
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21 <param name="sequence" value="2" />
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22 <param name="quality" value="3" />
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23 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
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24 </test>
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25 <!-- color space test -->
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26 <test>
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27 <param name="input_file" value="fastq_to_tabular_out_2.tabular" ftype="tabular" />
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28 <param name="identifier" value="1" />
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29 <param name="sequence" value="2" />
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30 <param name="quality" value="3" />
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31 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
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32 </test>
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33 </tests>
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34 <help>
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35 **What it does**
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36
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37 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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39 ------
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40
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41 **Citation**
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42
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43 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;`_
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45
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46 </help>
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47 </tool>