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1 <tool id="tab2fasta" name="Tabular-to-FASTA" version="1.1.0">
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2 <description>converts tabular file to FASTA format</description>
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3 <command interpreter="python">tabular_to_fasta.py $input $title_col $seq_col $output </command>
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4 <inputs>
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5 <param name="input" type="data" format="tabular" label="Tab-delimited file"/>
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6 <param name="title_col" type="data_column" data_ref="input" multiple="True" numerical="False" label="Title column(s)" help="Multi-select list - hold the appropriate key while clicking to select multiple columns"/>
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7 <param name="seq_col" type="data_column" data_ref="input" numerical="False" label="Sequence column" />
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8 </inputs>
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9 <outputs>
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10 <data name="output" format="fasta"/>
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11 </outputs>
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12 <tests>
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13 <test>
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14 <param name="input" value="solexa.tabular" />
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15 <param name="title_col" value="1,2,3,4" />
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16 <param name="seq_col" value="5" />
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17 <output name="output" file="tabular_to_fasta_out1.fasta" />
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18 </test>
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19 </tests>
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20 <help>
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21
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22 **What it does**
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23
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24 Converts tab delimited data into FASTA formatted sequences.
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25
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26 -----------
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27
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28 **Example**
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29
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30 Suppose this is a sequence file produced by Illumina (Solexa) sequencer::
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31
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32 5 300 902 419 GACTCATGATTTCTTACCTATTAGTGGTTGAACATC
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33 5 300 880 431 GTGATATGTATGTTGACGGCCATAAGGCTGCTTCTT
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34
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35 Selecting **c3** and **c4** as the **Title column(s)** and **c5** as the **Sequence column** will result in::
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36
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37 >902_419
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38 GACTCATGATTTCTTACCTATTAGTGGTTGAACATC
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39 >880_431
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40 GTGATATGTATGTTGACGGCCATAAGGCTGCTTCTT
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41
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42 </help>
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43 </tool> |
