[2] | 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> |
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