diff tabular_to_fasta.xml @ 0:db61adc12770 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tabular_to_fasta.xml	Mon May 19 10:59:53 2014 -0400
@@ -0,0 +1,43 @@
+<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>
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