view tabular_to_fasta.xml @ 0:db61adc12770 draft

Imported from capsule None

<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::

	&gt;902_419
	GACTCATGATTTCTTACCTATTAGTGGTTGAACATC
	&gt;880_431
	GTGATATGTATGTTGACGGCCATAAGGCTGCTTCTT
	
	</help>
</tool>