mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-16 15:45:04 +08:00
43 lines
1.4 KiB
XML
43 lines
1.4 KiB
XML
<tool id="tab2fasta" name="Tabular-to-FASTA" version="1.1.0">
|
|
<description>converts tabular file to FASTA format</description>
|
|
<command interpreter="python">tabular_to_fasta.py $input $title_col $seq_col $output </command>
|
|
<inputs>
|
|
<param name="input" type="data" format="tabular" label="Tab-delimited file"/>
|
|
<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"/>
|
|
<param name="seq_col" type="data_column" data_ref="input" numerical="False" label="Sequence column" />
|
|
</inputs>
|
|
<outputs>
|
|
<data name="output" format="fasta"/>
|
|
</outputs>
|
|
<tests>
|
|
<test>
|
|
<param name="input" value="solexa.tabular" />
|
|
<param name="title_col" value="1,2,3,4" />
|
|
<param name="seq_col" value="5" />
|
|
<output name="output" file="tabular_to_fasta_out1.fasta" />
|
|
</test>
|
|
</tests>
|
|
<help>
|
|
|
|
**What it does**
|
|
|
|
Converts tab delimited data into FASTA formatted sequences.
|
|
|
|
-----------
|
|
|
|
**Example**
|
|
|
|
Suppose this is a sequence file produced by Illumina (Solexa) sequencer::
|
|
|
|
5 300 902 419 GACTCATGATTTCTTACCTATTAGTGGTTGAACATC
|
|
5 300 880 431 GTGATATGTATGTTGACGGCCATAAGGCTGCTTCTT
|
|
|
|
Selecting **c3** and **c4** as the **Title column(s)** and **c5** as the **Sequence column** will result in::
|
|
|
|
>902_419
|
|
GACTCATGATTTCTTACCTATTAGTGGTTGAACATC
|
|
>880_431
|
|
GTGATATGTATGTTGACGGCCATAAGGCTGCTTCTT
|
|
|
|
</help>
|
|
</tool> |