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annotate tabular_to_fastq.xml @ 1:7bde4f066435 draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:45:21 -0400
parents 9ae652b76979
children 643018aa1435
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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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38
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39 </help>
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40
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41 <citations>
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42 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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43 </citations>
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44
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45 </tool>